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annotate hubArchiveCreator.xml @ 9:d5781fe7b782 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
author yating-l
date Wed, 28 Dec 2016 17:33:08 -0500
parents be8fd2f24c60
children 364b8db8de17
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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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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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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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67 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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69 #set temp_max_digit = 0
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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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77 #set nb_digits_max_track = len(str($temp_max_digit))
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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($nb_digits_max_track)
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87 ## For each format, we have a few mandatory fields we store in a dict
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88 #set track_color = str($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
9
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114 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
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115 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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116 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
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117 extra_data_dict)
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118 #end if
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119 #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option"
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120 --bigpsl $f.formatChoice.bedChoice.bigPsl
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121 #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final,
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122 extra_data_dict)
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123 #end if
0
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124 #end if
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125 #if $f.formatChoice.format_select == "psl"
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126 --psl $f.formatChoice.PSL
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127 #silent $prepare_json($f.formatChoice.PSL, $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 == "bigwig"
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131 --bigwig $f.formatChoice.BIGWIG
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132 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
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133 extra_data_dict)
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134 #end if
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135 #if $f.formatChoice.format_select == "gff3"
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136 --gff3 $f.formatChoice.GFF3
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137 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
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138 extra_data_dict)
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139 #end if
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140 #if $f.formatChoice.format_select == "gtf"
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141 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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142 --gtf $f.formatChoice.GTF
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143 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
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144 extra_data_dict)
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145 #end if
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146 #end for
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147 #end for
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148
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149 ## We combine the fasta file dataset name with his false path in a JSON object
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150 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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151 -f '$fasta_json'
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152
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153 ## Dump the final json
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154 #set all_data_json = json.dumps($data_parameter_dict)
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155
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156 --data_json '$all_data_json'
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157
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158 ## Retrieve the user email
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159 --user_email $__user_email__
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160
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161 -d $__tool_directory__
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162
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163 -e $output.extra_files_path
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164
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165 $advanced_options.debug_mode
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166
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167 -o $output;
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168
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169 ]]></command>
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170
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171 <inputs>
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172 <param
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173 name="genome_name"
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174 type="text"
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175 size="30"
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176 value="unknown"
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177 label="UCSC Genome Browser assembly ID"
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178 />
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179 <param
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180 format="fasta"
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181 name="fasta_file"
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diff changeset
182 type="data"
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183 label="Reference genome"
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184 />
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185 <repeat name="group" title="New group">
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186 <param type="text" name="group_name" label="Group name" value="Default group"/>
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187 <repeat name="format" title="New track">
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188 <conditional name="formatChoice">
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189 <param name="format_select" type="select" label="Format">
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190 <option value="bam" selected="true">BAM</option>
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191 <option value="bed">BED</option>
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192 <option value="psl">PSL</option>
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193 <option value="bigwig">BIGWIG</option>
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194 <option value="gff3">GFF3</option>
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195 <option value="gtf">GTF</option>
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196 </param>
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197
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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198 <when value="bam">
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diff changeset
199 <param
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200 format="bam"
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201 name="BAM"
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202 type="data"
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203 label="BAM File"
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204 />
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205 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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206 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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207 <sanitizer>
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208 <valid initial="string.letters,string.digits">
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diff changeset
209 <add value="#"/>
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210 </valid>
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211 </sanitizer>
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diff changeset
212 </param>
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213 </when>
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214 <when value="bed">
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215 <conditional name="bedChoice">
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216 <param name="bed_select" type="select" label="Bed Choice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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217 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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218 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
9
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219 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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220 <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
221 </param>
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parents:
diff changeset
222 <when value="bed_generic">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
223 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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224 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
225 name="BED"
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diff changeset
226 type="data"
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diff changeset
227 label="Generic Bed File Choice"
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228 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
229
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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230 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
231 <when value="bed_simple_repeats_option">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
232 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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233 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
234 name="BED_simple_repeats"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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235 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
236 label="Bed Simple Repeats (Bed4+12) File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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237 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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238 </when>
9
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diff changeset
239 <when value="bed_splice_junctions_option">
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diff changeset
240 <param
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241 format="bed"
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diff changeset
242 name="BED_splice_junctions"
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diff changeset
243 type="data"
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diff changeset
244 label="Bed Splice Junctions (Bed12+1) File"
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245 />
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246 </when>
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diff changeset
247 <when value="bigpsl_option">
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diff changeset
248 <param
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249 format="bed"
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diff changeset
250 name="bigPsl"
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diff changeset
251 type="data"
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diff changeset
252 label="bigPsl (Bed12+12) File"
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diff changeset
253 />
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254 </when>
0
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255 </conditional>
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256 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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257 <sanitizer>
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258 <valid initial="string.letters,string.digits">
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parents:
diff changeset
259 <add value="#"/>
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260 </valid>
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261 </sanitizer>
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262 </param>
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263 </when>
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264 <when value="psl">
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265 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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266 format="psl"
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diff changeset
267 name="PSL"
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268 type="data"
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diff changeset
269 label="PSL File"
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diff changeset
270 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
271 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
272 <sanitizer>
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diff changeset
273 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
274 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
275 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
276 </sanitizer>
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diff changeset
277 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
278 </when>
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yating-l
parents:
diff changeset
279 <when value="bigwig">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
280 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
281 format="bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
282 name="BIGWIG"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
283 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
284 label="BIGWIG File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
285 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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286 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
287 <sanitizer>
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288 <valid initial="string.letters,string.digits">
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289 <add value="#"/>
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290 </valid>
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291 </sanitizer>
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292 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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293 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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294 <when value="gff3">
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diff changeset
295 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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296 format="gff3"
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diff changeset
297 name="GFF3"
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diff changeset
298 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
299 label="GFF3 File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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300 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
301 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
302 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
303 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
304 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
305 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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306 </sanitizer>
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diff changeset
307 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
308 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
309 <when value="gtf">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
310 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
311 format="gtf"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
312 name="GTF"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
313 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
314 label="GTF File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
315 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
316 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
317 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
318 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
319 <add value="#"/>
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diff changeset
320 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
321 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
322 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
323 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
324 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
325 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
326 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
327 <conditional name="advanced_options">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
328 <param name="advanced_options_selector" type="select" label="Advanced options">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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329 <option value="off" selected="true">Hide advanced options</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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330 <option value="on">Display advanced options</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
331 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
332 <!-- TODO: Avoid redundancy here -->
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diff changeset
333 <when value="on">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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334 <param name="debug_mode" type="boolean"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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335 label="Activate debug mode" checked="false"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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336 truevalue="--debug_mode" falsevalue="">
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337 <help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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338 Use this option if you are a G-OnRamp developer
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339 </help>
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340 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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341 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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342 <when value="off">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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343 <param name="debug_mode" type="hidden"
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diff changeset
344 value="">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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345 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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346 </when>
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347 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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348 </inputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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349
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
350 <outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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351 <data format="trackhub" name="output"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
352 </outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
353
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
354 <tests>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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355 <!-- Test with only the fasta file -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
356 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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357 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
358 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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diff changeset
359 <output name="output" file="only_genome/only_genome.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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360 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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diff changeset
361 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
362 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
363 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
364 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
365 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
366 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
367 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
368 </extra_files>
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yating-l
parents:
diff changeset
369 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
370 </extra_files>
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yating-l
parents:
diff changeset
371 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
372 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
373 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
374
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
375 <!-- Test with Bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
376 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
377 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
378 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
379 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
380 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
381 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
382 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
383 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
384 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
385 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
386 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
387 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
388 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
389 <output name="output" file="bam/bam.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
390 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
391 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
392 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
393 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
394 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
395 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
396 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
397 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
398 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
399 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
400 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
401 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
402 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
403 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
404 <has_text text="track"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
405 <has_text text="longLabel"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
406 <has_text text="shortLabel"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
407 <has_text text="bigDataUrl"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
408 <has_text text="type"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
409 <has_text text="visibility"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
410 <has_text text="thickDrawItem"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
411 <has_text text="priority"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
412 <has_text text="color"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
413 <has_text text="group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
414 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
415 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
416 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
417 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
418 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
419
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
420 <!-- Test with Bed Generic -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
421 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
422 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
423 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
424 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
425 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
426 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
427 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
428 <param name="format_select" value="bed" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
429 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
430 <param name="bed_select" value="bed_generic"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
431 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
432 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
433 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
434 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
435 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
436 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
437 <output name="output" file="bed_generic/bed_generic.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
438 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
439 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
440 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
441 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
442 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
443 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
444 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
445 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
446
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
447 <!-- Test with Bed Simple repeat -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
448 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
449 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
450 <param name="fasta_file" value="common/dbia3.fa"/>
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parents:
diff changeset
451 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
452 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
453 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
454 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
455 <param name="format_select" value="bed" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
456 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
457 <param name="bed_select" value="bed_simple_repeats_option"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
458 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
459 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
460 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
461 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
462 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
463 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
464 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
465 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
466 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
467 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
468 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
469 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
470 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
471 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
472 </test>
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
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parents: 8
diff changeset
473
2
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yating-l
parents: 0
diff changeset
474
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
475 <!-- Test with Psl -->
2
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yating-l
parents: 0
diff changeset
476 <test>
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yating-l
parents: 0
diff changeset
477 <param name="genome_name" value="Dbia3"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
478 <param name="fasta_file" value="common/dbia3.fa"/>
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yating-l
parents: 0
diff changeset
479 <repeat name="group">
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yating-l
parents: 0
diff changeset
480 <param name="group_name" value="Default group"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
481 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
482 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
483 <param name="format_select" value="psl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
484 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
485 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
486 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
487 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
488 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
489 <output name="output" file="psl/psl_trackhub.html">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
490 <!-- Verify tracks folder contains bam and bai -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
491 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
492 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
493 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
494 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
495 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
496 <!-- Verify trackDb.txt contains the basic fields for a bam -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
497 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
498 </output>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
499 </test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
500
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
501 <!-- Test with BigWig -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
502 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
503 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
504 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
505 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
506 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
507 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
508 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
509 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
510 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
511 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
512 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
513 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
514 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
515 <output name="output" file="bigwig/bigwig.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
516 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
517 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
518 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
519 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
520 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
521 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
522 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
523 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
524 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
525 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
526
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
527 <!-- Test with GFF3 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
528 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
529 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
530 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
531 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
532 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
533 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
534 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
535 <param name="format_select" value="gff3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
536 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
537 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
538 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
539 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
540 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
541 <output name="output" file="gff3/gff3_trackhub.html">
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yating-l
parents:
diff changeset
542 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
543 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
544 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
545 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
546 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
547 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
548 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
549 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
550 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
551 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
552
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
553 <!-- Test with GTF -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
554 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
555 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
556 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
557 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
558 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
559 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
560 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
561 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
562 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
563 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
564 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
565 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
566 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
567 <output name="output" file="gtf/gtf_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
568 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
569 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
570 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
571 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
572 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
573 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
574 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
575 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
576 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
577 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
578
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
579 <!-- Test with one group and multiple tracks -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
580 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
581 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
582 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
583 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
584 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
585 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
586 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
587 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
588 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
589 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
590 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
591 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
592 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
593 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
594 <param name="format_select" value="gff3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
595 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
596 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
597 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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diff changeset
598 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
599 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
600 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
601 <!-- verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
602 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
603 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
604 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
605 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
606 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
607 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
608 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
609 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
610 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
611 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
612 <!-- verify trackdb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
613 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
614 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
615 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
616
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
diff changeset
617 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
2
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parents: 0
diff changeset
618 <test>
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yating-l
parents: 0
diff changeset
619 <param name="genome_name" value="Dbia3"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
620 <param name="fasta_file" value="common/dbia3.fa"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
621 <repeat name="group">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
622 <param name="group_name" value="Default group"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
623 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
624 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
625 <param name="format_select" value="bam"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
626 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
627 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
628 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
629 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
630 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
631 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
632 <param name="format_select" value="bed"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
633 <conditional name="bedChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
634 <param name="bed_select" value="bed_generic"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
635 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
636 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
637 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
638 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
639 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
640 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
641 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
642 <param name="format_select" value="bed"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
643 <conditional name="bedChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
644 <param name="bed_select" value="bed_simple_repeats_option"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
645 <param name="BED_simple_repeats" ftype="bed"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
646 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
647 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
648 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
649 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
650 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
651 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
652 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
653 <param name="format_select" value="psl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
654 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
655 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
656 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
657 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
658 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
659 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
660 <param name="format_select" value="bigwig"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
661 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
662 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
663 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
664 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
665 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
666 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
667 <param name="format_select" value="gff3"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
668 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
669 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
670 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
671 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
672 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
673 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
674 <param name="format_select" value="gtf"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
675 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
676 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
677 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
678 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
679 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
680 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
681 <!-- verify tracks folder contains all the files -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
682 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
683 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
684 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
685 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
686 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
687 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
688 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
689 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
690 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
691 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
692 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
693 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
694 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
695 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
696 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
697 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
698 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
699 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
700 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
701 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
702 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
703 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
704 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
705 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
706 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
707 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
708 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
709 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
710 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
711 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
712 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
713 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
714 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
715 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
716 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
717 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
718 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
719 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
720 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
721 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
722 <!-- verify trackdb.txt contains the basic fields for a bam -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
723 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
724 </output>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
725 </test>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
726
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
727 <!-- Test with two groups and no tracks -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
728 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
729 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
730 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
731 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
732 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
733 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
734 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
735 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
736 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
737 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
738 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
739 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
740 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
741 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
742 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
743 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
744 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
745 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
746 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
747 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
748 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
749 value="two_groups_no_track/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
750 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
751 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
752
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
753 <!-- Test with two groups and one track in first -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
754 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
755 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
756 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
757 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
758 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
759 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
760 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
761 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
762 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
763 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
764 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
765 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
766 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
767 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
768 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
769 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
770 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
771 <!-- Check myHub structure -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
772 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
773 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
774 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
775 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
776 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
777 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
778 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
779 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
780 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
781 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
782 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
783 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
784
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
785 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
786 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
787 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
788 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
789 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
790 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
791
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
792 <!-- Check the groups.txt exists and is properly populated -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
793 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
794 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
795
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
796 <!-- Test with two groups and one track in both -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
797 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
798 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
799 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
800 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
801 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
802 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
803 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
804 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
805 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
806 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
807 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
808 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
809 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
810 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
811 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
812 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
813 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
814 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
815 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
816 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
817 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
818 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
819 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
820 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
821 <!-- Check myHub structure -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
822 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
823 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
824 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
825 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
826 lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
827 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
828 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
829 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
830 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
831 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
832 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
833 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
834 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
835
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
836 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
837 <!-- First group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
838 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
839 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
840 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
841 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
842 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
843
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
844 <!-- Second group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
845 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
846 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
847 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
848 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
849 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
850 <!-- Check the groups.txt exists and is properly populated -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
851 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
852 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
853
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
854 <!-- Test with two groups and multiple tracks in both -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
855 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
856 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
857 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
858 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
859 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
860 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
861 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
862 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
863 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
864 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
865 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
866 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
867 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
868 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
869 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
870 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
871 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
872 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
873 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
874 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
875 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
876 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
877 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
878 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
879 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
880 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
881 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
882 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
883 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
884 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
885 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
886 <param name="format_select" value="gff3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
887 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
888 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
889 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
890 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
891 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
892 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
893 <!-- Check myHub structure -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
894 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
895 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
896 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
897 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
898 lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
899 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
900 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
901 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
902 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
903 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
904 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
905 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
906 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
907
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
908 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
909 <!-- First group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
910 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
911 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
912 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
913 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
914 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
915 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
916 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
917 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
918 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
919 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
920 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
921 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
922 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
923 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
924 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
925
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
926 <!-- Second group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
927 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
928 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
929 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
930 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
931 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
932 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
933 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
934 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
935 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
936 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
937 <!-- Check the groups.txt exists and is properly populated -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
938 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
939 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
940
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
941 <!-- Test default color in a track -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
942 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
943 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
944 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
945 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
946 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
947 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
948 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
949 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
950 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
951 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
952 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
953 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
954 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
955 <output name="output" file="default_color/default_color_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
956 <!-- Verify trackDb.txt contains the color 0,0,0 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
957 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
958 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
959 <has_text text="color 0,0,0"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
960 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
961 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
962
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
963 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
964 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
965 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
966
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
967 <!-- Test changed color in a track -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
968 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
969 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
970 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
971 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
972 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
973 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
974 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
975 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
976 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
977 <param name="track_color" value="#8064a2"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
978 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
979 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
980 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
981 <output name="output" file="changed_color/changed_color_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
982 <!-- Verify trackDb.txt contains the color 128,100,162 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
983 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
984 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
985 <has_text text="color 128,100,162"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
986 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
987 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
988
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989 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
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990 </output>
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991 </test>
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992
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993 <!-- Test for StringTie Chromosome end coordinates -->
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994 <test>
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995 <param name="genome_name" value="Dbia3"/>
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996 <param name="fasta_file" value="common/dbia3.fa"/>
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997 <repeat name="group">
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998 <param name="group_name" value="Default group"/>
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999 <repeat name="format">
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1000 <conditional name="formatChoice">
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1001 <param name="format_select" value="gtf"/>
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1002 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
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1003 <param name="track_color" value="#000000"/>
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1004 </conditional>
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1005 </repeat>
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1006 </repeat>
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1007 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
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1008 <extra_files type="file"
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1009 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
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1010 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
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1011 compare="sim_size"
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1012 />
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1013
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1014 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
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1015 </output>
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1016 </test>
2
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1017
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1018 <!-- Test for big files? -->
0
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1019
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1020 <!-- Find tests that should fail -->
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1021
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1022 </tests>
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1023
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1024 <help>
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1025 This Galaxy tool permits to prepare your files to be ready for
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1026 Assembly Hub visualization.
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1027 </help>
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1028 </tool>