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annotate hubArchiveCreator.xml @ 0:abcfd662b679 draft default tip

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author yating-l
date Thu, 22 Dec 2016 17:53:00 -0500
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
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2 <description>
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3 This Galaxy tool permits to prepare your files to be ready for
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4 Assembly Hub visualization.
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5 </description>
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6
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7 <requirements>
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8 <!-- Conda dependencies -->
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9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
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10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
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11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>
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12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
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13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
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14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
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15 <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
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16 <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
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17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
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18 <requirement type="package" version="1.3">samtools</requirement>
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19 <!-- ToolShed dependencies -->
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20 <requirement type="package" version="312">ucsc_tools</requirement>
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21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
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22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
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23 <requirement type="package" version="0.0.1">genePredToBed</requirement>
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24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
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25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
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26 <requirement type="package" version="1.2">samtools</requirement>
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27 </requirements>
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28
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29 <stdio>
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30 <regex match="^pass1"
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31 source="stderr"
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32 level="log"
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33 description="bedToBigBed"/>
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34 <!-- TODO: Add the case pass1 and 0 chroms -->
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35 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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36 </stdio>
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37
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38 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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39 <command detect_errors="exit_code"><![CDATA[
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40 mkdir -p $output.extra_files_path;
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41
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42 python $__tool_directory__/hubArchiveCreator.py
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44 ## Ask the user to enter the genome name
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45 --genome_name '$genome_name'
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46
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47 #import json
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48
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49 #set global data_parameter_dict = {}
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50
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51 ## Function to retrieve the data of the inputs
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52 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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53 #set false_path = str($input_to_prepare)
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54 #set name = $input_to_prepare.name
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55
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56 #set data_dict = {"name": $name}
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57 #silent data_dict.update($extra_data_dict)
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58
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59 ## Add the ordering by taking the tool form indexes
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60 #silent $data_dict.update({"order_index": $order_index})
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62 #silent $data_parameter_dict.update({$false_path: $data_dict})
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64 #end def
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65
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67 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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68
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69 #set temp_max_digit = 0
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70
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71 #for $g in $group
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72 #if len($g.format) > $temp_max_digit
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73 #silent temp_max_digit = len($g.format)
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74 #end if
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75 #end for
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76
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77 #set nb_digits_max_track = len(str($temp_max_digit))
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78
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79 ## END Get the number of digits
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80
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81 #for $i_g, $g in enumerate( $group )
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82 #for $i, $f in enumerate( $g.format )
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83 ## Create the order index using index_group+1 concatenated with index_track
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84 #set index_group_final = str($i_g + 1)
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85 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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86
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87 ## For each format, we have a few mandatory fields we store in a dict
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88 #set track_color = str($f.formatChoice.track_color)
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89 #set group_name = str($g.group_name)
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90
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91 #set extra_data_dict = {"track_color": $track_color,
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92 "group_name": $group_name}
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93
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94 #if $f.formatChoice.format_select == "bam"
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95 --bam $f.formatChoice.BAM
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96 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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97
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98 ## Add Bam format specific fields
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99 #silent extra_data_dict.update({"index": $bam_index})
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100
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101 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
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102 #end if
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103 #if $f.formatChoice.format_select == "bed"
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104 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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105 --bed $f.formatChoice.bedChoice.BED
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106 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
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107 extra_data_dict)
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108 #end if
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109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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112 extra_data_dict)
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113 #end if
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114 #end if
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115 #if $f.formatChoice.format_select == "psl"
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116 --psl $f.formatChoice.PSL
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117 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
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118 extra_data_dict)
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119 #end if
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120 #if $f.formatChoice.format_select == "bigwig"
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121 --bigwig $f.formatChoice.BIGWIG
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122 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
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123 extra_data_dict)
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124 #end if
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125 #if $f.formatChoice.format_select == "gff3"
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126 --gff3 $f.formatChoice.GFF3
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127 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
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128 extra_data_dict)
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129 #end if
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130 #if $f.formatChoice.format_select == "gtf"
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131 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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132 --gtf $f.formatChoice.GTF
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133 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
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134 extra_data_dict)
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135 #end if
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136 #end for
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137 #end for
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138
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139 ## We combine the fasta file dataset name with his false path in a JSON object
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140 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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141 -f '$fasta_json'
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142
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143 ## Dump the final json
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144 #set all_data_json = json.dumps($data_parameter_dict)
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145
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146 --data_json '$all_data_json'
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147
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148 ## Retrieve the user email
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149 --user_email $__user_email__
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150
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151 -d $__tool_directory__
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152
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153 -e $output.extra_files_path
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154
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155 $advanced_options.debug_mode
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156
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157 -o $output;
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158
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159 ]]></command>
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160
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161 <inputs>
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162 <param
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163 name="genome_name"
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164 type="text"
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165 size="30"
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166 value="unknown"
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167 label="UCSC Genome Browser assembly ID"
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168 />
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169 <param
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170 format="fasta"
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171 name="fasta_file"
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172 type="data"
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173 label="Reference genome"
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174 />
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175 <repeat name="group" title="New group">
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176 <param type="text" name="group_name" label="Group name" value="Default group"/>
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177 <repeat name="format" title="New track">
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178 <conditional name="formatChoice">
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179 <param name="format_select" type="select" label="Format">
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180 <option value="bam" selected="true">BAM</option>
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181 <option value="bed">BED</option>
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182 <option value="psl">PSL</option>
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183 <option value="bigwig">BIGWIG</option>
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184 <option value="gff3">GFF3</option>
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185 <option value="gtf">GTF</option>
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186 </param>
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187
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188 <when value="bam">
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189 <param
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190 format="bam"
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191 name="BAM"
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192 type="data"
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193 label="BAM File"
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194 />
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195 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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196 <param name="track_color" type="color" label="Track color" value="#000000">
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197 <sanitizer>
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198 <valid initial="string.letters,string.digits">
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199 <add value="#"/>
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200 </valid>
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201 </sanitizer>
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202 </param>
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203 </when>
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204 <when value="bed">
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205 <conditional name="bedChoice">
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206 <param name="bed_select" type="select" label="Bed Choice">
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207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
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208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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209 </param>
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210 <when value="bed_generic">
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211 <param
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212 format="bed"
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213 name="BED"
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214 type="data"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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215 label="Generic Bed File Choice"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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216 />
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217
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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218 </when>
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219 <when value="bed_simple_repeats_option">
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220 <param
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221 format="bed"
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222 name="BED_simple_repeats"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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223 type="data"
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224 label="Bed Simple Repeats (Bed4+12) File"
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225 />
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226 </when>
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227 </conditional>
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228 <param name="track_color" type="color" label="Track color" value="#000000">
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229 <sanitizer>
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230 <valid initial="string.letters,string.digits">
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231 <add value="#"/>
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232 </valid>
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233 </sanitizer>
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234 </param>
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235 </when>
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236 <when value="psl">
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237 <param
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238 format="psl"
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239 name="PSL"
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240 type="data"
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241 label="PSL File"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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242 />
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243 <param name="track_color" type="color" label="Track color" value="#000000">
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244 <sanitizer>
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245 <valid initial="string.letters,string.digits">
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246 <add value="#"/>
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247 </valid>
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248 </sanitizer>
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249 </param>
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250 </when>
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251 <when value="bigwig">
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252 <param
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253 format="bigwig"
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254 name="BIGWIG"
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255 type="data"
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256 label="BIGWIG File"
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257 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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258 <param name="track_color" type="color" label="Track color" value="#000000">
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259 <sanitizer>
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260 <valid initial="string.letters,string.digits">
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261 <add value="#"/>
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262 </valid>
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263 </sanitizer>
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264 </param>
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265 </when>
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266 <when value="gff3">
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267 <param
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268 format="gff3"
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269 name="GFF3"
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270 type="data"
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271 label="GFF3 File"
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272 />
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273 <param name="track_color" type="color" label="Track color" value="#000000">
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274 <sanitizer>
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275 <valid initial="string.letters,string.digits">
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276 <add value="#"/>
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277 </valid>
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278 </sanitizer>
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279 </param>
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280 </when>
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281 <when value="gtf">
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282 <param
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283 format="gtf"
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284 name="GTF"
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285 type="data"
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286 label="GTF File"
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287 />
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288 <param name="track_color" type="color" label="Track color" value="#000000">
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289 <sanitizer>
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290 <valid initial="string.letters,string.digits">
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291 <add value="#"/>
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292 </valid>
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293 </sanitizer>
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294 </param>
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295 </when>
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296 </conditional>
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297 </repeat>
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298 </repeat>
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299 <conditional name="advanced_options">
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300 <param name="advanced_options_selector" type="select" label="Advanced options">
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301 <option value="off" selected="true">Hide advanced options</option>
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302 <option value="on">Display advanced options</option>
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303 </param>
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304 <!-- TODO: Avoid redundancy here -->
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305 <when value="on">
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306 <param name="debug_mode" type="boolean"
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307 label="Activate debug mode" checked="false"
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308 truevalue="--debug_mode" falsevalue="">
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309 <help>
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310 Use this option if you are a G-OnRamp developer
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311 </help>
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312 </param>
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313 </when>
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314 <when value="off">
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315 <param name="debug_mode" type="hidden"
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316 value="">
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317 </param>
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318 </when>
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319 </conditional>
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320 </inputs>
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321
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322 <outputs>
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323 <data format="trackhub" name="output"/>
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324 </outputs>
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325
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326 <tests>
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327 <!-- Test with only the fasta file -->
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328 <test>
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329 <param name="genome_name" value="Dbia3"/>
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330 <param name="fasta_file" value="common/dbia3.fa"/>
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331 <output name="output" file="only_genome/only_genome.html">
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332 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
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333 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
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334 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
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335 <!-- Email could be different, but we need to ensure we still have the email line -->
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336 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
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337 <assert_contents>
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338 <has_text text="email"/>
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339 </assert_contents>
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340 </extra_files>
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341 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
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342 </extra_files>
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343 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
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344 </output>
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345 </test>
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346
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347 <!-- Test with Bam -->
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348 <test>
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349 <param name="genome_name" value="Dbia3"/>
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350 <param name="fasta_file" value="common/dbia3.fa"/>
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351 <repeat name="group">
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352 <param name="group_name" value="Default group"/>
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353 <repeat name="format">
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354 <conditional name="formatChoice">
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355 <param name="format_select" value="bam"/>
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356 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
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357 <param name="track_color" value="#000000"/>
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358 </conditional>
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359 </repeat>
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360 </repeat>
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361 <output name="output" file="bam/bam.html">
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362 <!-- Verify tracks folder contains bam and bai -->
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363 <extra_files type="file"
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364 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
365 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
366 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
367 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
368 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
369 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
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diff changeset
370 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
371 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
372 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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373 <!-- Verify trackDb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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374 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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375 <assert_contents>
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376 <has_text text="track"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
377 <has_text text="longLabel"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
378 <has_text text="shortLabel"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
379 <has_text text="bigDataUrl"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
380 <has_text text="type"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
381 <has_text text="visibility"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
382 <has_text text="thickDrawItem"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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383 <has_text text="priority"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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384 <has_text text="color"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
385 <has_text text="group"/>
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386 </assert_contents>
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387 </extra_files>
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388 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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389 </output>
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390 </test>
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391
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
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392 <!-- Test with Bed Generic -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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393 <test>
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394 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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395 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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396 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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397 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
398 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
399 <conditional name="formatChoice">
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400 <param name="format_select" value="bed" />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
401 <conditional name="bedChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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402 <param name="bed_select" value="bed_generic"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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403 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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404 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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405 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
406 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
407 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
408 </repeat>
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409 <output name="output" file="bed_generic/bed_generic.html">
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410 <!-- Verify tracks folder contains bam and bai -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
411 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
412 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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413 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
414 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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415 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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416 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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417 </test>
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418
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419 <!-- Test with Bed Simple repeat -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
420 <test>
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421 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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422 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
423 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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424 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
425 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
426 <conditional name="formatChoice">
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diff changeset
427 <param name="format_select" value="bed" />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
428 <conditional name="bedChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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429 <param name="bed_select" value="bed_simple_repeats_option"/>
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430 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
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431 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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432 </conditional>
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433 </conditional>
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434 </repeat>
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435 </repeat>
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436 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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437 <!-- Verify tracks folder contains bam and bai -->
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diff changeset
438 <extra_files type="file"
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439 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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440 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
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diff changeset
441 compare="sim_size"
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diff changeset
442 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
443 </output>
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diff changeset
444 </test>
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diff changeset
445
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446 <!-- Test with Psl -->
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diff changeset
447 <test>
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448 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
449 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
450 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
451 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
452 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
453 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
454 <param name="format_select" value="psl"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
455 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
456 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
457 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
458 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
459 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
460 <output name="output" file="psl/psl_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
461 <!-- Verify tracks folder contains bam and bai -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
462 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
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diff changeset
463 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
464 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
465 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
466 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
467 <!-- Verify trackDb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
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diff changeset
468 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
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diff changeset
469 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
470 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
471
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
472 <!-- Test with BigWig -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
473 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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474 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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475 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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476 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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477 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
478 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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479 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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480 <param name="format_select" value="bigwig"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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481 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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482 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
483 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
484 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
485 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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486 <output name="output" file="bigwig/bigwig.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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487 <!-- Verify tracks folder contains bam and bai -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
488 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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489 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
490 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
491 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
492 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
493 <!-- Verify trackDb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
494 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
495 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
496 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
497
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
498 <!-- Test with GFF3 -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
499 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
500 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
501 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
502 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
503 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
504 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
505 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
506 <param name="format_select" value="gff3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
507 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
508 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
509 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
510 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
511 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
512 <output name="output" file="gff3/gff3_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
513 <!-- Verify tracks folder contains bam and bai -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
514 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
515 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
516 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
517 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
518 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
519 <!-- Verify trackDb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
520 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
521 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
522 </test>
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parents:
diff changeset
523
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
524 <!-- Test with GTF -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
525 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
526 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
527 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
528 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
529 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
530 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
531 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
532 <param name="format_select" value="gtf"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
533 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
534 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
535 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
536 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
537 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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diff changeset
538 <output name="output" file="gtf/gtf_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
539 <!-- Verify tracks folder contains bam and bai -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
540 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
541 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
542 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
543 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
544 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
545 <!-- Verify trackDb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
546 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
547 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
548 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
549
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
550 <!-- Test with one group and multiple tracks -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
551 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
552 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
553 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
554 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
555 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
556 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
557 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
558 <param name="format_select" value="gtf"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
559 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
560 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
561 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
562 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
563 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
564 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
565 <param name="format_select" value="gff3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
566 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
567 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
568 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
569 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
570 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
571 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
572 <!-- verify tracks folder contains bam and bai -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
573 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
574 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
575 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
576 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
577 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
578 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
579 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
580 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
581 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
582 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
583 <!-- verify trackdb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
584 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
585 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
586 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
587
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
588 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
589 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
590 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
591 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
592 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
593 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
594 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
595 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
596 <param name="format_select" value="bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
597 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
598 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
599 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
600 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
601 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
602 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
603 <param name="format_select" value="bed"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
604 <conditional name="bedChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
605 <param name="bed_select" value="bed_generic"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
606 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
607 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
608 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
609 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
610 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
611 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
612 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
613 <param name="format_select" value="bed"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
614 <conditional name="bedChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
615 <param name="bed_select" value="bed_simple_repeats_option"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
616 <param name="BED_simple_repeats" ftype="bed"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
617 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
618 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
619 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
620 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
621 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
622 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
623 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
624 <param name="format_select" value="psl"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
625 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
626 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
627 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
628 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
629 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
630 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
631 <param name="format_select" value="bigwig"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
632 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
633 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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parents:
diff changeset
634 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
635 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
636 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
637 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
638 <param name="format_select" value="gff3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
639 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
640 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
641 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
642 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
643 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
644 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
645 <param name="format_select" value="gtf"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
646 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
647 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
648 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
649 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
650 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
651 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
652 <!-- verify tracks folder contains all the files -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
653 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
654 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
655 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
656 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
657 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
658 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
659 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
660 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
661 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
662 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
663 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
664 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
665 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
666 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
667 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
668 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
669 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
670 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
671 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
672 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
673 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
674 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
675 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
676 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
677 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
678 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
679 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
680 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
681 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
682 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
683 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
684 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
685 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
686 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
687 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
688 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
689 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
690 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
691 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
692 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
693 <!-- verify trackdb.txt contains the basic fields for a bam -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
694 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
695 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
696 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
697
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
698 <!-- Test with two groups and no tracks -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
699 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
700 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
701 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
702 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
703 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
704 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
705 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
706 <param name="group_name" value="Other group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
707 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
708 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
709 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
710 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
711 <!-- Email could be different, but we need to ensure we still have the email line -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
712 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
713 <assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
714 <has_text text="email"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
715 </assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
716 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
717 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
718 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
719 <extra_files type="file" name="myHub/Dbia3/description.html"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
720 value="two_groups_no_track/myHub/Dbia3/description.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
721 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
722 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
723
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
724 <!-- Test with two groups and one track in first -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
725 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
726 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
727 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
728 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
729 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
730 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
731 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
732 <param name="format_select" value="bigwig"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
733 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
734 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
735 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
736 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
737 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
738 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
739 <param name="group_name" value="Other group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
740 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
741 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
742 <!-- Check myHub structure -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
743 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
744 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
745 <!-- Email could be different, but we need to ensure we still have the email line -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
746 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
747 <assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
748 <has_text text="email"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
749 </assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
750 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
751 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
752 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
753 <extra_files type="file" name="myHub/Dbia3/description.html"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
754 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
755
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
756 <!-- Check tracks exist -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
757 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
758 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
759 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
760 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
761 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
762
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
763 <!-- Check the groups.txt exists and is properly populated -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
764 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
765 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
766
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
767 <!-- Test with two groups and one track in both -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
768 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
769 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
770 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
771 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
772 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
773 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
774 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
775 <param name="format_select" value="bigwig"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
776 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
777 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
778 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
779 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
780 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
781 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
782 <param name="group_name" value="Other group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
783 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
784 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
785 <param name="format_select" value="gtf"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
786 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
787 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
788 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
789 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
790 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
791 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
792 <!-- Check myHub structure -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
793 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
794 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
795 <!-- Email could be different, but we need to ensure we still have the email line -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
796 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
797 lines_diff="2">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
798 <assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
799 <has_text text="email"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
800 </assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
801 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
802 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
803 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
804 <extra_files type="file" name="myHub/Dbia3/description.html"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
805 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
806
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
807 <!-- Check tracks exist -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
808 <!-- First group -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
809 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
810 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
811 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
812 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
813 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
814
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
815 <!-- Second group -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
816 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
817 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
818 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
819 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
820 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
821 <!-- Check the groups.txt exists and is properly populated -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
822 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
823 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
824
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
825 <!-- Test with two groups and multiple tracks in both -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
826 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
827 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
828 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
829 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
830 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
831 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
832 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
833 <param name="format_select" value="bigwig"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
834 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
835 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
836 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
837 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
838 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
839 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
840 <param name="format_select" value="bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
841 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
842 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
843 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
844 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
845 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
846 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
847 <param name="group_name" value="Other group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
848 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
849 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
850 <param name="format_select" value="gtf"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
851 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
852 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
853 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
854 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
855 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
856 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
857 <param name="format_select" value="gff3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
858 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
859 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
860 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
861 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
862 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
863 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
864 <!-- Check myHub structure -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
865 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
866 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
867 <!-- Email could be different, but we need to ensure we still have the email line -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
868 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
869 lines_diff="2">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
870 <assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
871 <has_text text="email"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
872 </assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
873 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
874 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
875 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
876 <extra_files type="file" name="myHub/Dbia3/description.html"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
877 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
878
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
879 <!-- Check tracks exist -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
880 <!-- First group -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
881 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
882 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
883 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
884 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
885 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
886 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
887 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
888 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
889 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
890 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
891 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
892 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
893 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
894 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
895 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
896
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
897 <!-- Second group -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
898 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
899 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
900 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
901 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
902 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
903 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
904 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
905 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
906 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
907 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
908 <!-- Check the groups.txt exists and is properly populated -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
909 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
910 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
911
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
912 <!-- Test default color in a track -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
913 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
914 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
915 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
916 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
917 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
918 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
919 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
920 <param name="format_select" value="bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
921 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
922 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
923 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
924 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
925 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
926 <output name="output" file="default_color/default_color_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
927 <!-- Verify trackDb.txt contains the color 0,0,0 -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
928 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
929 <assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
930 <has_text text="color 0,0,0"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
931 </assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
932 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
933
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
934 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
935 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
936 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
937
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
938 <!-- Test changed color in a track -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
939 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
940 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
941 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
942 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
943 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
944 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
945 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
946 <param name="format_select" value="bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
947 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
948 <param name="track_color" value="#8064a2"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
949 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
950 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
951 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
952 <output name="output" file="changed_color/changed_color_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
953 <!-- Verify trackDb.txt contains the color 128,100,162 -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
954 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
955 <assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
956 <has_text text="color 128,100,162"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
957 </assert_contents>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
958 </extra_files>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
959
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
960 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
961 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
962 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
963
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
964 <!-- Test for StringTie Chromosome end coordinates -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
965 <test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
966 <param name="genome_name" value="Dbia3"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
967 <param name="fasta_file" value="common/dbia3.fa"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
968 <repeat name="group">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
969 <param name="group_name" value="Default group"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
970 <repeat name="format">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
971 <conditional name="formatChoice">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
972 <param name="format_select" value="gtf"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
973 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
974 <param name="track_color" value="#000000"/>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
975 </conditional>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
976 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
977 </repeat>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
978 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
979 <extra_files type="file"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
980 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
981 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
982 compare="sim_size"
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
983 />
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
984
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
985 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
986 </output>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
987 </test>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
yating-l
parents:
diff changeset
988
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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989 <!-- Test for big files? -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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990
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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991 <!-- Find tests that should fail -->
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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992
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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993 </tests>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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994
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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995 <help>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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996 This Galaxy tool permits to prepare your files to be ready for
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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997 Assembly Hub visualization.
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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998 </help>
abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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999 </tool>