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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
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2 <description>
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3 This Galaxy tool permits to prepare your files to be ready for
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4 Assembly Hub visualization.
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5 </description>
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6
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7 <requirements>
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8 <!-- Conda dependencies -->
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9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
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10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
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11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>
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12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
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13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
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14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
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15 <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
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16 <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
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17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
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18 <requirement type="package" version="1.3">samtools</requirement>
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19 <!-- ToolShed dependencies -->
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20 <requirement type="package" version="312">ucsc_tools</requirement>
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21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
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22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
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23 <requirement type="package" version="0.0.1">genePredToBed</requirement>
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24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
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25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
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26 <requirement type="package" version="1.2">samtools</requirement>
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27 </requirements>
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28
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29 <stdio>
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30 <regex match="^pass1"
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31 source="stderr"
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32 level="log"
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33 description="bedToBigBed"/>
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34 <!-- TODO: Add the case pass1 and 0 chroms -->
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35 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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36 </stdio>
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37
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38 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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39 <command detect_errors="exit_code"><![CDATA[
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40 mkdir -p $output.extra_files_path;
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41
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42 python $__tool_directory__/hubArchiveCreator.py
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43
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44 ## Ask the user to enter the genome name
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45 --genome_name '$genome_name'
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46
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47 #import json
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48
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49 #set global data_parameter_dict = {}
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50
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51 ## Function to retrieve the data of the inputs
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52 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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53 #set false_path = str($input_to_prepare)
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54 #set name = $input_to_prepare.name
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55
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56 #set data_dict = {"name": $name}
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57 #silent data_dict.update($extra_data_dict)
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58
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59 ## Add the ordering by taking the tool form indexes
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60 #silent $data_dict.update({"order_index": $order_index})
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61
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62 #silent $data_parameter_dict.update({$false_path: $data_dict})
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63
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64 #end def
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65
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66
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67 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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68
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69 #set temp_max_digit = 0
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70
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71 #for $g in $group
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72 #if len($g.format) > $temp_max_digit
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73 #silent temp_max_digit = len($g.format)
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74 #end if
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75 #end for
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76
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77 #set nb_digits_max_track = len(str($temp_max_digit))
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78
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79 ## END Get the number of digits
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80
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81 #for $i_g, $g in enumerate( $group )
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82 #for $i, $f in enumerate( $g.format )
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83 ## Create the order index using index_group+1 concatenated with index_track
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84 #set index_group_final = str($i_g + 1)
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85 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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86
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87 ## For each format, we have a few mandatory fields we store in a dict
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88 #set track_color = str($f.formatChoice.track_color)
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89 #set group_name = str($g.group_name)
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90
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91 #set extra_data_dict = {"track_color": $track_color,
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92 "group_name": $group_name}
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93
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94 #if $f.formatChoice.format_select == "bam"
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95 --bam $f.formatChoice.BAM
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96 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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97
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98 ## Add Bam format specific fields
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99 #silent extra_data_dict.update({"index": $bam_index})
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100
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101 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
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102 #end if
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103 #if $f.formatChoice.format_select == "bed"
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104 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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105 --bed $f.formatChoice.bedChoice.BED
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106 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
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107 extra_data_dict)
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108 #end if
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109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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112 extra_data_dict)
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113 #end if
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114 #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 #end if
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120 #if $f.formatChoice.format_select == "psl"
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121 --psl $f.formatChoice.PSL
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122 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
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123 extra_data_dict)
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124 #end if
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125 #if $f.formatChoice.format_select == "bigwig"
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126 --bigwig $f.formatChoice.BIGWIG
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127 #silent $prepare_json($f.formatChoice.BIGWIG, $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 == "gff3"
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131 --gff3 $f.formatChoice.GFF3
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132 #silent $prepare_json($f.formatChoice.GFF3, $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 == "gtf"
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136 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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137 --gtf $f.formatChoice.GTF
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138 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
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139 extra_data_dict)
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140 #end if
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141 #end for
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142 #end for
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143
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144 ## We combine the fasta file dataset name with his false path in a JSON object
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145 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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146 -f '$fasta_json'
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147
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148 ## Dump the final json
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149 #set all_data_json = json.dumps($data_parameter_dict)
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150
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151 --data_json '$all_data_json'
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152
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153 ## Retrieve the user email
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154 --user_email $__user_email__
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155
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156 -d $__tool_directory__
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157
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158 -e $output.extra_files_path
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159
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160 $advanced_options.debug_mode
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161
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162 -o $output;
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163
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164 ]]></command>
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165
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166 <inputs>
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167 <param
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168 name="genome_name"
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169 type="text"
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170 size="30"
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171 value="unknown"
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172 label="UCSC Genome Browser assembly ID"
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173 />
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174 <param
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175 format="fasta"
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176 name="fasta_file"
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177 type="data"
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178 label="Reference genome"
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179 />
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180 <repeat name="group" title="New group">
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181 <param type="text" name="group_name" label="Group name" value="Default group"/>
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182 <repeat name="format" title="New track">
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183 <conditional name="formatChoice">
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184 <param name="format_select" type="select" label="Format">
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185 <option value="bam" selected="true">BAM</option>
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186 <option value="bed">BED</option>
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187 <option value="psl">PSL</option>
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188 <option value="bigwig">BIGWIG</option>
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189 <option value="gff3">GFF3</option>
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190 <option value="gtf">GTF</option>
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191 </param>
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192
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193 <when value="bam">
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194 <param
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195 format="bam"
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196 name="BAM"
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197 type="data"
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198 label="BAM File"
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199 />
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200 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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201 <param name="track_color" type="color" label="Track color" value="#000000">
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202 <sanitizer>
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203 <valid initial="string.letters,string.digits">
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204 <add value="#"/>
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205 </valid>
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206 </sanitizer>
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207 </param>
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208 </when>
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209 <when value="bed">
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210 <conditional name="bedChoice">
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211 <param name="bed_select" type="select" label="Bed Choice">
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212 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
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213 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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214 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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215 </param>
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216 <when value="bed_generic">
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217 <param
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218 format="bed"
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219 name="BED"
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220 type="data"
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221 label="Generic Bed File Choice"
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222 />
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223
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224 </when>
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225 <when value="bed_simple_repeats_option">
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226 <param
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227 format="bed"
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228 name="BED_simple_repeats"
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229 type="data"
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230 label="Bed Simple Repeats (Bed4+12) File"
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231 />
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232 </when>
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233 <when value="bed_splice_junctions_option">
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234 <param
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235 format="bed"
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236 name="BED_splice_junctions"
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237 type="data"
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238 label="Bed Splice Junctions (Bed12+1) File"
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239 />
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240 </when>
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241 </conditional>
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242 <param name="track_color" type="color" label="Track color" value="#000000">
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243 <sanitizer>
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244 <valid initial="string.letters,string.digits">
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245 <add value="#"/>
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246 </valid>
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247 </sanitizer>
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248 </param>
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249 </when>
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250 <when value="psl">
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251 <param
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252 format="psl"
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253 name="PSL"
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254 type="data"
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255 label="PSL File"
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256 />
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257 <param name="track_color" type="color" label="Track color" value="#000000">
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258 <sanitizer>
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259 <valid initial="string.letters,string.digits">
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260 <add value="#"/>
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261 </valid>
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262 </sanitizer>
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263 </param>
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264 </when>
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265 <when value="bigwig">
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266 <param
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267 format="bigwig"
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268 name="BIGWIG"
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269 type="data"
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270 label="BIGWIG File"
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271 />
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272 <param name="track_color" type="color" label="Track color" value="#000000">
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273 <sanitizer>
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274 <valid initial="string.letters,string.digits">
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275 <add value="#"/>
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276 </valid>
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277 </sanitizer>
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278 </param>
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279 </when>
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280 <when value="gff3">
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281 <param
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282 format="gff3"
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283 name="GFF3"
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284 type="data"
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285 label="GFF3 File"
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286 />
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287 <param name="track_color" type="color" label="Track color" value="#000000">
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288 <sanitizer>
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289 <valid initial="string.letters,string.digits">
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290 <add value="#"/>
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291 </valid>
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292 </sanitizer>
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293 </param>
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294 </when>
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295 <when value="gtf">
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296 <param
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297 format="gtf"
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298 name="GTF"
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299 type="data"
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300 label="GTF File"
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301 />
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302 <param name="track_color" type="color" label="Track color" value="#000000">
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303 <sanitizer>
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304 <valid initial="string.letters,string.digits">
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305 <add value="#"/>
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306 </valid>
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307 </sanitizer>
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308 </param>
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309 </when>
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310 </conditional>
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311 </repeat>
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312 </repeat>
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313 <conditional name="advanced_options">
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314 <param name="advanced_options_selector" type="select" label="Advanced options">
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315 <option value="off" selected="true">Hide advanced options</option>
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316 <option value="on">Display advanced options</option>
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317 </param>
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318 <!-- TODO: Avoid redundancy here -->
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319 <when value="on">
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320 <param name="debug_mode" type="boolean"
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321 label="Activate debug mode" checked="false"
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322 truevalue="--debug_mode" falsevalue="">
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323 <help>
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324 Use this option if you are a G-OnRamp developer
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325 </help>
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326 </param>
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327 </when>
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328 <when value="off">
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329 <param name="debug_mode" type="hidden"
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330 value="">
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331 </param>
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332 </when>
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333 </conditional>
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334 </inputs>
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335
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336 <outputs>
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337 <data format="trackhub" name="output"/>
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338 </outputs>
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339
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340 <tests>
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341 <!-- Test with only the fasta file -->
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342 <test>
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343 <param name="genome_name" value="Dbia3"/>
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344 <param name="fasta_file" value="common/dbia3.fa"/>
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345 <output name="output" file="only_genome/only_genome.html">
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346 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
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347 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
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348 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
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349 <!-- Email could be different, but we need to ensure we still have the email line -->
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350 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
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351 <assert_contents>
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352 <has_text text="email"/>
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353 </assert_contents>
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354 </extra_files>
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355 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
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356 </extra_files>
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357 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
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358 </output>
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359 </test>
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360
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361 <!-- Test with Bam -->
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362 <test>
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363 <param name="genome_name" value="Dbia3"/>
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364 <param name="fasta_file" value="common/dbia3.fa"/>
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365 <repeat name="group">
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366 <param name="group_name" value="Default group"/>
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367 <repeat name="format">
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368 <conditional name="formatChoice">
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369 <param name="format_select" value="bam"/>
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370 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
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371 <param name="track_color" value="#000000"/>
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372 </conditional>
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373 </repeat>
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374 </repeat>
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375 <output name="output" file="bam/bam.html">
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376 <!-- Verify tracks folder contains bam and bai -->
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377 <extra_files type="file"
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378 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
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379 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
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380 compare="sim_size"
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381 />
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382 <extra_files type="file"
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383 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
|
|
|
384 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
|
|
|
385 compare="sim_size"
|
|
|
386 />
|
|
|
387 <!-- Verify trackDb.txt contains the basic fields for a bam -->
|
|
|
388 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
|
|
|
389 <assert_contents>
|
|
|
390 <has_text text="track"/>
|
|
|
391 <has_text text="longLabel"/>
|
|
|
392 <has_text text="shortLabel"/>
|
|
|
393 <has_text text="bigDataUrl"/>
|
|
|
394 <has_text text="type"/>
|
|
|
395 <has_text text="visibility"/>
|
|
|
396 <has_text text="thickDrawItem"/>
|
|
|
397 <has_text text="priority"/>
|
|
|
398 <has_text text="color"/>
|
|
|
399 <has_text text="group"/>
|
|
|
400 </assert_contents>
|
|
|
401 </extra_files>
|
|
|
402 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
403 </output>
|
|
|
404 </test>
|
|
|
405
|
|
|
406 <!-- Test with Bed Generic -->
|
|
|
407 <test>
|
|
|
408 <param name="genome_name" value="Dbia3"/>
|
|
|
409 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
410 <repeat name="group">
|
|
|
411 <param name="group_name" value="Default group"/>
|
|
|
412 <repeat name="format">
|
|
|
413 <conditional name="formatChoice">
|
|
|
414 <param name="format_select" value="bed" />
|
|
|
415 <conditional name="bedChoice">
|
|
|
416 <param name="bed_select" value="bed_generic"/>
|
|
|
417 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
|
|
|
418 <param name="track_color" value="#000000"/>
|
|
|
419 </conditional>
|
|
|
420 </conditional>
|
|
|
421 </repeat>
|
|
|
422 </repeat>
|
|
|
423 <output name="output" file="bed_generic/bed_generic.html">
|
|
|
424 <!-- Verify tracks folder contains bam and bai -->
|
|
|
425 <extra_files type="file"
|
|
|
426 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
|
|
|
427 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
|
|
|
428 compare="sim_size"
|
|
|
429 />
|
|
|
430 </output>
|
|
|
431 </test>
|
|
|
432
|
|
|
433 <!-- Test with Bed Simple repeat -->
|
|
|
434 <test>
|
|
|
435 <param name="genome_name" value="Dbia3"/>
|
|
|
436 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
437 <repeat name="group">
|
|
|
438 <param name="group_name" value="Default group"/>
|
|
|
439 <repeat name="format">
|
|
|
440 <conditional name="formatChoice">
|
|
|
441 <param name="format_select" value="bed" />
|
|
|
442 <conditional name="bedChoice">
|
|
|
443 <param name="bed_select" value="bed_simple_repeats_option"/>
|
|
|
444 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
|
|
|
445 <param name="track_color" value="#000000"/>
|
|
|
446 </conditional>
|
|
|
447 </conditional>
|
|
|
448 </repeat>
|
|
|
449 </repeat>
|
|
|
450 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
|
|
|
451 <!-- Verify tracks folder contains bam and bai -->
|
|
|
452 <extra_files type="file"
|
|
|
453 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
|
|
|
454 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
|
|
|
455 compare="sim_size"
|
|
|
456 />
|
|
|
457 </output>
|
|
|
458 </test>
|
|
|
459
|
|
|
460
|
|
|
461 <!-- Test with Psl -->
|
|
|
462 <test>
|
|
|
463 <param name="genome_name" value="Dbia3"/>
|
|
|
464 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
465 <repeat name="group">
|
|
|
466 <param name="group_name" value="Default group"/>
|
|
|
467 <repeat name="format">
|
|
|
468 <conditional name="formatChoice">
|
|
|
469 <param name="format_select" value="psl"/>
|
|
|
470 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
|
|
|
471 <param name="track_color" value="#000000"/>
|
|
|
472 </conditional>
|
|
|
473 </repeat>
|
|
|
474 </repeat>
|
|
|
475 <output name="output" file="psl/psl_trackhub.html">
|
|
|
476 <!-- Verify tracks folder contains bam and bai -->
|
|
|
477 <extra_files type="file"
|
|
|
478 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
|
|
|
479 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
|
|
|
480 compare="sim_size"
|
|
|
481 />
|
|
|
482 <!-- Verify trackDb.txt contains the basic fields for a bam -->
|
|
|
483 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
484 </output>
|
|
|
485 </test>
|
|
|
486
|
|
|
487 <!-- Test with BigWig -->
|
|
|
488 <test>
|
|
|
489 <param name="genome_name" value="Dbia3"/>
|
|
|
490 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
491 <repeat name="group">
|
|
|
492 <param name="group_name" value="Default group"/>
|
|
|
493 <repeat name="format">
|
|
|
494 <conditional name="formatChoice">
|
|
|
495 <param name="format_select" value="bigwig"/>
|
|
|
496 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
|
|
|
497 <param name="track_color" value="#000000"/>
|
|
|
498 </conditional>
|
|
|
499 </repeat>
|
|
|
500 </repeat>
|
|
|
501 <output name="output" file="bigwig/bigwig.html">
|
|
|
502 <!-- Verify tracks folder contains bam and bai -->
|
|
|
503 <extra_files type="file"
|
|
|
504 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
505 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
506 compare="sim_size"
|
|
|
507 />
|
|
|
508 <!-- Verify trackDb.txt contains the basic fields for a bam -->
|
|
|
509 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
510 </output>
|
|
|
511 </test>
|
|
|
512
|
|
|
513 <!-- Test with GFF3 -->
|
|
|
514 <test>
|
|
|
515 <param name="genome_name" value="Dbia3"/>
|
|
|
516 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
517 <repeat name="group">
|
|
|
518 <param name="group_name" value="Default group"/>
|
|
|
519 <repeat name="format">
|
|
|
520 <conditional name="formatChoice">
|
|
|
521 <param name="format_select" value="gff3"/>
|
|
|
522 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
|
|
|
523 <param name="track_color" value="#000000"/>
|
|
|
524 </conditional>
|
|
|
525 </repeat>
|
|
|
526 </repeat>
|
|
|
527 <output name="output" file="gff3/gff3_trackhub.html">
|
|
|
528 <!-- Verify tracks folder contains bam and bai -->
|
|
|
529 <extra_files type="file"
|
|
|
530 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
|
|
|
531 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
|
|
|
532 compare="sim_size"
|
|
|
533 />
|
|
|
534 <!-- Verify trackDb.txt contains the basic fields for a bam -->
|
|
|
535 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
536 </output>
|
|
|
537 </test>
|
|
|
538
|
|
|
539 <!-- Test with GTF -->
|
|
|
540 <test>
|
|
|
541 <param name="genome_name" value="Dbia3"/>
|
|
|
542 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
543 <repeat name="group">
|
|
|
544 <param name="group_name" value="Default group"/>
|
|
|
545 <repeat name="format">
|
|
|
546 <conditional name="formatChoice">
|
|
|
547 <param name="format_select" value="gtf"/>
|
|
|
548 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
|
|
|
549 <param name="track_color" value="#000000"/>
|
|
|
550 </conditional>
|
|
|
551 </repeat>
|
|
|
552 </repeat>
|
|
|
553 <output name="output" file="gtf/gtf_trackhub.html">
|
|
|
554 <!-- Verify tracks folder contains bam and bai -->
|
|
|
555 <extra_files type="file"
|
|
|
556 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
557 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
558 compare="sim_size"
|
|
|
559 />
|
|
|
560 <!-- Verify trackDb.txt contains the basic fields for a bam -->
|
|
|
561 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
562 </output>
|
|
|
563 </test>
|
|
|
564
|
|
|
565 <!-- Test with one group and multiple tracks -->
|
|
|
566 <test>
|
|
|
567 <param name="genome_name" value="Dbia3"/>
|
|
|
568 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
569 <repeat name="group">
|
|
|
570 <param name="group_name" value="Default group"/>
|
|
|
571 <repeat name="format">
|
|
|
572 <conditional name="formatChoice">
|
|
|
573 <param name="format_select" value="gtf"/>
|
|
|
574 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
|
|
|
575 <param name="track_color" value="#000000"/>
|
|
|
576 </conditional>
|
|
|
577 </repeat>
|
|
|
578 <repeat name="format">
|
|
|
579 <conditional name="formatChoice">
|
|
|
580 <param name="format_select" value="gff3"/>
|
|
|
581 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
|
|
|
582 <param name="track_color" value="#000000"/>
|
|
|
583 </conditional>
|
|
|
584 </repeat>
|
|
|
585 </repeat>
|
|
|
586 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
|
|
|
587 <!-- verify tracks folder contains bam and bai -->
|
|
|
588 <extra_files type="file"
|
|
|
589 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
590 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
591 compare="sim_size"
|
|
|
592 />
|
|
|
593 <extra_files type="file"
|
|
|
594 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
|
|
|
595 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
|
|
|
596 compare="sim_size"
|
|
|
597 />
|
|
|
598 <!-- verify trackdb.txt contains the basic fields for a bam -->
|
|
|
599 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
600 </output>
|
|
|
601 </test>
|
|
|
602
|
|
|
603 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
|
|
|
604 <test>
|
|
|
605 <param name="genome_name" value="Dbia3"/>
|
|
|
606 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
607 <repeat name="group">
|
|
|
608 <param name="group_name" value="Default group"/>
|
|
|
609 <repeat name="format">
|
|
|
610 <conditional name="formatChoice">
|
|
|
611 <param name="format_select" value="bam"/>
|
|
|
612 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
|
|
|
613 <param name="track_color" value="#000000"/>
|
|
|
614 </conditional>
|
|
|
615 </repeat>
|
|
|
616 <repeat name="format">
|
|
|
617 <conditional name="formatChoice">
|
|
|
618 <param name="format_select" value="bed"/>
|
|
|
619 <conditional name="bedChoice">
|
|
|
620 <param name="bed_select" value="bed_generic"/>
|
|
|
621 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
|
|
|
622 <param name="track_color" value="#000000"/>
|
|
|
623 </conditional>
|
|
|
624 </conditional>
|
|
|
625 </repeat>
|
|
|
626 <repeat name="format">
|
|
|
627 <conditional name="formatChoice">
|
|
|
628 <param name="format_select" value="bed"/>
|
|
|
629 <conditional name="bedChoice">
|
|
|
630 <param name="bed_select" value="bed_simple_repeats_option"/>
|
|
|
631 <param name="BED_simple_repeats" ftype="bed"
|
|
|
632 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
|
|
|
633 <param name="track_color" value="#000000"/>
|
|
|
634 </conditional>
|
|
|
635 </conditional>
|
|
|
636 </repeat>
|
|
|
637 <repeat name="format">
|
|
|
638 <conditional name="formatChoice">
|
|
|
639 <param name="format_select" value="psl"/>
|
|
|
640 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
|
|
|
641 <param name="track_color" value="#000000"/>
|
|
|
642 </conditional>
|
|
|
643 </repeat>
|
|
|
644 <repeat name="format">
|
|
|
645 <conditional name="formatChoice">
|
|
|
646 <param name="format_select" value="bigwig"/>
|
|
|
647 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
|
|
|
648 <param name="track_color" value="#000000"/>
|
|
|
649 </conditional>
|
|
|
650 </repeat>
|
|
|
651 <repeat name="format">
|
|
|
652 <conditional name="formatChoice">
|
|
|
653 <param name="format_select" value="gff3"/>
|
|
|
654 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
|
|
|
655 <param name="track_color" value="#000000"/>
|
|
|
656 </conditional>
|
|
|
657 </repeat>
|
|
|
658 <repeat name="format">
|
|
|
659 <conditional name="formatChoice">
|
|
|
660 <param name="format_select" value="gtf"/>
|
|
|
661 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
|
|
|
662 <param name="track_color" value="#000000"/>
|
|
|
663 </conditional>
|
|
|
664 </repeat>
|
|
|
665 </repeat>
|
|
|
666 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
|
|
|
667 <!-- verify tracks folder contains all the files -->
|
|
|
668 <extra_files type="file"
|
|
|
669 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
|
|
|
670 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
|
|
|
671 compare="sim_size"
|
|
|
672 />
|
|
|
673 <extra_files type="file"
|
|
|
674 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
|
|
|
675 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
|
|
|
676 compare="sim_size"
|
|
|
677 />
|
|
|
678 <extra_files type="file"
|
|
|
679 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
|
|
|
680 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
|
|
|
681 compare="sim_size"
|
|
|
682 />
|
|
|
683 <extra_files type="file"
|
|
|
684 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
|
|
|
685 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
|
|
|
686 compare="sim_size"
|
|
|
687 />
|
|
|
688 <extra_files type="file"
|
|
|
689 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
|
|
|
690 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
|
|
|
691 compare="sim_size"
|
|
|
692 />
|
|
|
693 <extra_files type="file"
|
|
|
694 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
695 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
696 compare="sim_size"
|
|
|
697 />
|
|
|
698 <extra_files type="file"
|
|
|
699 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
|
|
|
700 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
|
|
|
701 compare="sim_size"
|
|
|
702 />
|
|
|
703 <extra_files type="file"
|
|
|
704 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
705 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
706 compare="sim_size"
|
|
|
707 />
|
|
|
708 <!-- verify trackdb.txt contains the basic fields for a bam -->
|
|
|
709 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
710 </output>
|
|
|
711 </test>
|
|
|
712
|
|
|
713 <!-- Test with two groups and no tracks -->
|
|
|
714 <test>
|
|
|
715 <param name="genome_name" value="Dbia3"/>
|
|
|
716 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
717 <repeat name="group">
|
|
|
718 <param name="group_name" value="Default group"/>
|
|
|
719 </repeat>
|
|
|
720 <repeat name="group">
|
|
|
721 <param name="group_name" value="Other group"/>
|
|
|
722 </repeat>
|
|
|
723 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
|
|
|
724 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
|
|
|
725 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
|
|
|
726 <!-- Email could be different, but we need to ensure we still have the email line -->
|
|
|
727 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
|
|
|
728 <assert_contents>
|
|
|
729 <has_text text="email"/>
|
|
|
730 </assert_contents>
|
|
|
731 </extra_files>
|
|
|
732 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
|
|
|
733 </extra_files>
|
|
|
734 <extra_files type="file" name="myHub/Dbia3/description.html"
|
|
|
735 value="two_groups_no_track/myHub/Dbia3/description.html"/>
|
|
|
736 </output>
|
|
|
737 </test>
|
|
|
738
|
|
|
739 <!-- Test with two groups and one track in first -->
|
|
|
740 <test>
|
|
|
741 <param name="genome_name" value="Dbia3"/>
|
|
|
742 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
743 <repeat name="group">
|
|
|
744 <param name="group_name" value="Default group"/>
|
|
|
745 <repeat name="format">
|
|
|
746 <conditional name="formatChoice">
|
|
|
747 <param name="format_select" value="bigwig"/>
|
|
|
748 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
|
|
|
749 <param name="track_color" value="#000000"/>
|
|
|
750 </conditional>
|
|
|
751 </repeat>
|
|
|
752 </repeat>
|
|
|
753 <repeat name="group">
|
|
|
754 <param name="group_name" value="Other group"/>
|
|
|
755 </repeat>
|
|
|
756 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
|
|
|
757 <!-- Check myHub structure -->
|
|
|
758 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
|
|
|
759 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
|
|
|
760 <!-- Email could be different, but we need to ensure we still have the email line -->
|
|
|
761 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
|
|
|
762 <assert_contents>
|
|
|
763 <has_text text="email"/>
|
|
|
764 </assert_contents>
|
|
|
765 </extra_files>
|
|
|
766 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
|
|
|
767 </extra_files>
|
|
|
768 <extra_files type="file" name="myHub/Dbia3/description.html"
|
|
|
769 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
|
|
|
770
|
|
|
771 <!-- Check tracks exist -->
|
|
|
772 <extra_files type="file"
|
|
|
773 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
774 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
775 compare="sim_size"
|
|
|
776 />
|
|
|
777
|
|
|
778 <!-- Check the groups.txt exists and is properly populated -->
|
|
|
779 </output>
|
|
|
780 </test>
|
|
|
781
|
|
|
782 <!-- Test with two groups and one track in both -->
|
|
|
783 <test>
|
|
|
784 <param name="genome_name" value="Dbia3"/>
|
|
|
785 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
786 <repeat name="group">
|
|
|
787 <param name="group_name" value="Default group"/>
|
|
|
788 <repeat name="format">
|
|
|
789 <conditional name="formatChoice">
|
|
|
790 <param name="format_select" value="bigwig"/>
|
|
|
791 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
|
|
|
792 <param name="track_color" value="#000000"/>
|
|
|
793 </conditional>
|
|
|
794 </repeat>
|
|
|
795 </repeat>
|
|
|
796 <repeat name="group">
|
|
|
797 <param name="group_name" value="Other group"/>
|
|
|
798 <repeat name="format">
|
|
|
799 <conditional name="formatChoice">
|
|
|
800 <param name="format_select" value="gtf"/>
|
|
|
801 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
|
|
|
802 <param name="track_color" value="#000000"/>
|
|
|
803 </conditional>
|
|
|
804 </repeat>
|
|
|
805 </repeat>
|
|
|
806 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
|
|
|
807 <!-- Check myHub structure -->
|
|
|
808 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
|
|
|
809 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
|
|
|
810 <!-- Email could be different, but we need to ensure we still have the email line -->
|
|
|
811 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
|
|
|
812 lines_diff="2">
|
|
|
813 <assert_contents>
|
|
|
814 <has_text text="email"/>
|
|
|
815 </assert_contents>
|
|
|
816 </extra_files>
|
|
|
817 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
|
|
|
818 </extra_files>
|
|
|
819 <extra_files type="file" name="myHub/Dbia3/description.html"
|
|
|
820 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
|
|
|
821
|
|
|
822 <!-- Check tracks exist -->
|
|
|
823 <!-- First group -->
|
|
|
824 <extra_files type="file"
|
|
|
825 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
826 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
827 compare="sim_size"
|
|
|
828 />
|
|
|
829
|
|
|
830 <!-- Second group -->
|
|
|
831 <extra_files type="file"
|
|
|
832 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
833 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
834 compare="sim_size"
|
|
|
835 />
|
|
|
836 <!-- Check the groups.txt exists and is properly populated -->
|
|
|
837 </output>
|
|
|
838 </test>
|
|
|
839
|
|
|
840 <!-- Test with two groups and multiple tracks in both -->
|
|
|
841 <test>
|
|
|
842 <param name="genome_name" value="Dbia3"/>
|
|
|
843 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
844 <repeat name="group">
|
|
|
845 <param name="group_name" value="Default group"/>
|
|
|
846 <repeat name="format">
|
|
|
847 <conditional name="formatChoice">
|
|
|
848 <param name="format_select" value="bigwig"/>
|
|
|
849 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
|
|
|
850 <param name="track_color" value="#000000"/>
|
|
|
851 </conditional>
|
|
|
852 </repeat>
|
|
|
853 <repeat name="format">
|
|
|
854 <conditional name="formatChoice">
|
|
|
855 <param name="format_select" value="bam"/>
|
|
|
856 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
|
|
|
857 <param name="track_color" value="#000000"/>
|
|
|
858 </conditional>
|
|
|
859 </repeat>
|
|
|
860 </repeat>
|
|
|
861 <repeat name="group">
|
|
|
862 <param name="group_name" value="Other group"/>
|
|
|
863 <repeat name="format">
|
|
|
864 <conditional name="formatChoice">
|
|
|
865 <param name="format_select" value="gtf"/>
|
|
|
866 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
|
|
|
867 <param name="track_color" value="#000000"/>
|
|
|
868 </conditional>
|
|
|
869 </repeat>
|
|
|
870 <repeat name="format">
|
|
|
871 <conditional name="formatChoice">
|
|
|
872 <param name="format_select" value="gff3"/>
|
|
|
873 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
|
|
|
874 <param name="track_color" value="#000000"/>
|
|
|
875 </conditional>
|
|
|
876 </repeat>
|
|
|
877 </repeat>
|
|
|
878 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
|
|
|
879 <!-- Check myHub structure -->
|
|
|
880 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
|
|
|
881 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
|
|
|
882 <!-- Email could be different, but we need to ensure we still have the email line -->
|
|
|
883 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
|
|
|
884 lines_diff="2">
|
|
|
885 <assert_contents>
|
|
|
886 <has_text text="email"/>
|
|
|
887 </assert_contents>
|
|
|
888 </extra_files>
|
|
|
889 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
|
|
|
890 </extra_files>
|
|
|
891 <extra_files type="file" name="myHub/Dbia3/description.html"
|
|
|
892 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
|
|
|
893
|
|
|
894 <!-- Check tracks exist -->
|
|
|
895 <!-- First group -->
|
|
|
896 <extra_files type="file"
|
|
|
897 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
898 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
|
|
|
899 compare="sim_size"
|
|
|
900 />
|
|
|
901 <extra_files type="file"
|
|
|
902 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
|
|
|
903 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
|
|
|
904 compare="sim_size"
|
|
|
905 />
|
|
|
906 <extra_files type="file"
|
|
|
907 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
|
|
|
908 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
|
|
|
909 compare="sim_size"
|
|
|
910 />
|
|
|
911
|
|
|
912 <!-- Second group -->
|
|
|
913 <extra_files type="file"
|
|
|
914 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
915 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
916 compare="sim_size"
|
|
|
917 />
|
|
|
918 <extra_files type="file"
|
|
|
919 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
|
|
|
920 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
|
|
|
921 compare="sim_size"
|
|
|
922 />
|
|
|
923 <!-- Check the groups.txt exists and is properly populated -->
|
|
|
924 </output>
|
|
|
925 </test>
|
|
|
926
|
|
|
927 <!-- Test default color in a track -->
|
|
|
928 <test>
|
|
|
929 <param name="genome_name" value="Dbia3"/>
|
|
|
930 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
931 <repeat name="group">
|
|
|
932 <param name="group_name" value="Default group"/>
|
|
|
933 <repeat name="format">
|
|
|
934 <conditional name="formatChoice">
|
|
|
935 <param name="format_select" value="bam"/>
|
|
|
936 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
|
|
|
937 <param name="track_color" value="#000000"/>
|
|
|
938 </conditional>
|
|
|
939 </repeat>
|
|
|
940 </repeat>
|
|
|
941 <output name="output" file="default_color/default_color_trackhub.html">
|
|
|
942 <!-- Verify trackDb.txt contains the color 0,0,0 -->
|
|
|
943 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
|
|
|
944 <assert_contents>
|
|
|
945 <has_text text="color 0,0,0"/>
|
|
|
946 </assert_contents>
|
|
|
947 </extra_files>
|
|
|
948
|
|
|
949 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
950 </output>
|
|
|
951 </test>
|
|
|
952
|
|
|
953 <!-- Test changed color in a track -->
|
|
|
954 <test>
|
|
|
955 <param name="genome_name" value="Dbia3"/>
|
|
|
956 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
957 <repeat name="group">
|
|
|
958 <param name="group_name" value="Default group"/>
|
|
|
959 <repeat name="format">
|
|
|
960 <conditional name="formatChoice">
|
|
|
961 <param name="format_select" value="bam"/>
|
|
|
962 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
|
|
|
963 <param name="track_color" value="#8064a2"/>
|
|
|
964 </conditional>
|
|
|
965 </repeat>
|
|
|
966 </repeat>
|
|
|
967 <output name="output" file="changed_color/changed_color_trackhub.html">
|
|
|
968 <!-- Verify trackDb.txt contains the color 128,100,162 -->
|
|
|
969 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
|
|
|
970 <assert_contents>
|
|
|
971 <has_text text="color 128,100,162"/>
|
|
|
972 </assert_contents>
|
|
|
973 </extra_files>
|
|
|
974
|
|
|
975 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
976 </output>
|
|
|
977 </test>
|
|
|
978
|
|
|
979 <!-- Test for StringTie Chromosome end coordinates -->
|
|
|
980 <test>
|
|
|
981 <param name="genome_name" value="Dbia3"/>
|
|
|
982 <param name="fasta_file" value="common/dbia3.fa"/>
|
|
|
983 <repeat name="group">
|
|
|
984 <param name="group_name" value="Default group"/>
|
|
|
985 <repeat name="format">
|
|
|
986 <conditional name="formatChoice">
|
|
|
987 <param name="format_select" value="gtf"/>
|
|
|
988 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
|
|
|
989 <param name="track_color" value="#000000"/>
|
|
|
990 </conditional>
|
|
|
991 </repeat>
|
|
|
992 </repeat>
|
|
|
993 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
|
|
|
994 <extra_files type="file"
|
|
|
995 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
996 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
|
|
|
997 compare="sim_size"
|
|
|
998 />
|
|
|
999
|
|
|
1000 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
|
|
|
1001 </output>
|
|
|
1002 </test>
|
|
|
1003
|
|
|
1004 <!-- Test for big files? -->
|
|
|
1005
|
|
|
1006 <!-- Find tests that should fail -->
|
|
|
1007
|
|
|
1008 </tests>
|
|
|
1009
|
|
|
1010 <help>
|
|
|
1011 This Galaxy tool permits to prepare your files to be ready for
|
|
|
1012 Assembly Hub visualization.
|
|
|
1013 </help>
|
|
|
1014 </tool>
|
