Mercurial > repos > rmarenco > hubarchivecreator

annotate hubArchiveCreator.xml @ 23:2677f1899aa8 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author yating-l
date Tue, 09 May 2017 15:42:43 -0400
parents 7ddf651457df
children fcc1021bd496
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
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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 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
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9 <requirement type="package" version="1.2">samtools</requirement>
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10 </requirements>
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11
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12 <stdio>
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13 <regex match="^pass1"
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14 source="stderr"
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15 level="log"
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16 description="bedToBigBed"/>
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17 <!-- TODO: Add the case pass1 and 0 chroms -->
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18 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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19 </stdio>
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20
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21 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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22 <command detect_errors="exit_code"><![CDATA[
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23 mkdir -p $output.extra_files_path;
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24
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25 python $__tool_directory__/hubArchiveCreator.py
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27 ## Ask the user to enter the genome name
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28 --genome_name '$genome_name'
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29
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30 #import json
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31
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32 #set global data_parameter_dict = {}
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33
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34 ## Function to retrieve the data of the inputs
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35 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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36 #set false_path = str($input_to_prepare)
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37 #set name = $input_to_prepare.name
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38
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39 #set data_dict = {"name": $name}
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40 #silent data_dict.update($extra_data_dict)
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41
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42 ## Add the ordering by taking the tool form indexes
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43 #silent $data_dict.update({"order_index": $order_index})
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44
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45 #silent $data_parameter_dict.update({$false_path: $data_dict})
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46
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47 #end def
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48
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50 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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52 #set temp_max_digit = 0
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54 #for $g in $group
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55 #if len($g.format) > $temp_max_digit
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56 #silent temp_max_digit = len($g.format)
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57 #end if
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58 #end for
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60 #set nb_digits_max_track = len(str($temp_max_digit))
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62 ## END Get the number of digits
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63
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64 #for $i_g, $g in enumerate( $group )
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65 #for $i, $f in enumerate( $g.format )
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66 ## Create the order index using index_group+1 concatenated with index_track
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67 #set index_group_final = str($i_g + 1)
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68 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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70 ## For each format, we have a few mandatory fields we store in a dict
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71 #set track_color = str($f.formatChoice.track_color)
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72 #set group_name = str($g.group_name)
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73 #set longLabel = str($f.formatChoice.longLabel)
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74 #set extra_data_dict = {"track_color": $track_color,
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75 "group_name": $group_name,
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76 "long_label": $longLabel}
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78 #if $f.formatChoice.format_select == "bam"
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79 --bam $f.formatChoice.BAM
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80 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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81
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82 ## Add Bam format specific fields
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83 #silent extra_data_dict.update({"index": $bam_index})
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84
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85 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
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86 #end if
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87 #if $f.formatChoice.format_select == "bed"
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88 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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89 --bed $f.formatChoice.bedChoice.BED
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90 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
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91 extra_data_dict)
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92 #end if
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93 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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94 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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95 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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96 extra_data_dict)
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97 #end if
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98 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
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99 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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100 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
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101 extra_data_dict)
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102 #end if
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103 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
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104 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
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105 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
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106 extra_data_dict)
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107 #end if
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108 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
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109 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
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110 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
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111 extra_data_dict)
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112 #end if
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113 #end if
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114 #if $f.formatChoice.format_select == "psl"
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115 --psl $f.formatChoice.PSL
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116 #silent $prepare_json($f.formatChoice.PSL, $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.format_select == "bigwig"
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120 --bigwig $f.formatChoice.BIGWIG
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121 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
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122 extra_data_dict)
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123 #end if
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124 #if $f.formatChoice.format_select == "gff3"
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125 --gff3 $f.formatChoice.GFF3
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126 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
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127 extra_data_dict)
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128 #end if
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129 #if $f.formatChoice.format_select == "gtf"
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130 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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131 --gtf $f.formatChoice.GTF
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132 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
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133 extra_data_dict)
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134 #end if
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135 #end for
0
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136 #end for
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137
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138 ## We combine the fasta file dataset name with his false path in a JSON object
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139 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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140 -f '$fasta_json'
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141
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142 ## Dump the final json
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143 #set all_data_json = json.dumps($data_parameter_dict)
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144
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145 --data_json '$all_data_json'
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146
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147 ## Retrieve the user email
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148 --user_email $__user_email__
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149
13
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150 -d $__tool_directory__
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151
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152 -e $output.extra_files_path
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153
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154 $advanced_options.debug_mode
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155
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156 -o $output;
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157
0
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158 ]]></command>
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159
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160 <inputs>
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161 <param
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162 name="genome_name"
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163 type="text"
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164 size="30"
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165 value="unknown"
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166 label="UCSC Genome Browser assembly ID"
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167 />
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168 <param
0
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169 format="fasta"
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170 name="fasta_file"
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171 type="data"
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172 label="Reference genome"
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173 />
17
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174 <repeat name="group" title="New group">
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175 <param type="text" name="group_name" label="Group name" value="Default group"/>
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176 <repeat name="format" title="New track">
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177 <conditional name="formatChoice">
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178 <param name="format_select" type="select" label="Format">
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179 <option value="bam" selected="true">BAM</option>
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180 <option value="bed">BED</option>
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181 <option value="psl">PSL</option>
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182 <option value="bigwig">BIGWIG</option>
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183 <option value="gff3">GFF3</option>
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184 <option value="gtf">GTF</option>
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185 </param>
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186
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187 <when value="bam">
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188 <param
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189 format="bam"
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190 name="BAM"
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191 type="data"
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192 label="BAM File"
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193 />
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194 <param name="longLabel" type="text" size="80" label="Track label" />
17
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195 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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196 <param name="track_color" type="color" label="Track color" value="#000000">
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197 <sanitizer>
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198 <valid initial="string.letters,string.digits">
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199 <add value="#"/>
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200 </valid>
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201 </sanitizer>
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202 </param>
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203 </when>
17
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204 <when value="bed">
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205 <conditional name="bedChoice">
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206 <param name="bed_select" type="select" label="Bed Choice">
20
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207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
17
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208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
20
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209 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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210 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
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211 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
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212 </param>
20
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213 <when value="bed_generic">
17
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214 <param
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diff changeset
215 format="bed"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
216 name="BED"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
217 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
218 label="Generic Bed File Choice"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
219 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
220
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
221 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
222 <when value="bed_simple_repeats_option">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
223 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
224 format="bed"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
225 name="BED_simple_repeats"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
226 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
227 label="Bed Simple Repeats (Bed4+12) File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
228 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
229 </when>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
230 <when value="bed_splice_junctions_option">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
231 <param
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
232 format="bed"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
233 name="BED_splice_junctions"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
234 type="data"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
235 label="Bed Splice Junctions (Bed12+1) File"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
236 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
237 </when>
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
238 <when value="bed_blast_alignment_option">
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
239 <param
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
240 format="bed"
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
241 name="BED_blast_alignment"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
242 type="data"
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
243 label="Bed Blast Alignments (Bed12+12) File"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
244 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
245 </when>
22
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
246 <when value="bed_blat_alignment_option">
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
247 <param
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
248 format="bed"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
249 name="BED_blat_alignment"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
250 type="data"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
251 label="Bed BLAT Alignments (bigPsl) File"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
252 />
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
253 </when>
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
254 </conditional>
23
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 22
diff changeset
255 <param name="longLabel" type="text" size="30" label="Track name" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
256 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
257 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
258 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
259 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
260 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
261 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
262 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
263 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
264 <when value="psl">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
265 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
266 format="psl"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
267 name="PSL"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
268 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
269 label="PSL File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
270 />
23
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 22
diff changeset
271 <param name="longLabel" type="text" size="30" label="Track name" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
272 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
273 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
274 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
275 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
276 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
277 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
278 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
279 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
280 <when value="bigwig">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
281 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
282 format="bigwig"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
283 name="BIGWIG"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
284 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
285 label="BIGWIG File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
286 />
23
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 22
diff changeset
287 <param name="longLabel" type="text" size="30" label="Track name" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
288 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
289 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
290 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
291 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
292 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
293 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
294 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
295 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
296 <when value="gff3">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
297 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
298 format="gff3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
299 name="GFF3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
300 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
301 label="GFF3 File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
302 />
23
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 22
diff changeset
303 <param name="longLabel" type="text" size="30" label="Track name" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
304 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
305 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
306 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
307 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
308 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
309 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
310 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
311 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
312 <when value="gtf">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
313 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
314 format="gtf"
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315 name="GTF"
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316 type="data"
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317 label="GTF File"
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318 />
23
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319 <param name="longLabel" type="text" size="30" label="Track name" />
17
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320 <param name="track_color" type="color" label="Track color" value="#000000">
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321 <sanitizer>
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322 <valid initial="string.letters,string.digits">
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323 <add value="#"/>
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324 </valid>
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325 </sanitizer>
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326 </param>
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327 </when>
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328 </conditional>
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329 </repeat>
0
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330 </repeat>
13
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331 <conditional name="advanced_options">
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332 <param name="advanced_options_selector" type="select" label="Advanced options">
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333 <option value="off" selected="true">Hide advanced options</option>
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334 <option value="on">Display advanced options</option>
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335 </param>
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336 <!-- TODO: Avoid redundancy here -->
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337 <when value="on">
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338 <param name="debug_mode" type="boolean"
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339 label="Activate debug mode" checked="false"
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340 truevalue="--debug_mode" falsevalue="">
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341 <help>
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342 Use this option if you are a G-OnRamp developer
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343 </help>
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344 </param>
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345 </when>
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346 <when value="off">
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347 <param name="debug_mode" type="hidden"
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348 value="">
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349 </param>
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350 </when>
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351 </conditional>
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352 </inputs>
0
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353
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354 <outputs>
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355 <data format="trackhub" name="output"/>
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356 </outputs>
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357
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358 <tests>
20
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359 <!-- Test with only the fasta file -->
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360 <test>
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361 <param name="genome_name" value="Dbia3"/>
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362 <param name="fasta_file" value="common/dbia3.fa"/>
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363 <output name="output" file="only_genome/only_genome.html">
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364 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
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365 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
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366 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
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367 <!-- Email could be different, but we need to ensure we still have the email line -->
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368 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
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369 <assert_contents>
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370 <has_text text="email"/>
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371 </assert_contents>
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372 </extra_files>
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373 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
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374 </extra_files>
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375 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
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376 </output>
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377 </test>
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378
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379 <!-- Test with Bam -->
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380 <test>
20
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381 <param name="genome_name" value="Dbia3"/>
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382 <param name="fasta_file" value="common/dbia3.fa"/>
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383 <repeat name="group">
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384 <param name="group_name" value="Default group"/>
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385 <repeat name="format">
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386 <conditional name="formatChoice">
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387 <param name="format_select" value="bam"/>
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388 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
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389 <param name="track_color" value="#000000"/>
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390 </conditional>
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391 </repeat>
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392 </repeat>
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393 <output name="output" file="bam/bam.html">
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394 <!-- Verify tracks folder contains bam and bai -->
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yating-l
parents: 18
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395 <extra_files type="file"
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396 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
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397 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
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diff changeset
398 compare="sim_size"
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parents: 18
diff changeset
399 />
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parents: 18
diff changeset
400 <extra_files type="file"
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diff changeset
401 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
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402 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
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diff changeset
403 compare="sim_size"
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yating-l
parents: 18
diff changeset
404 />
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yating-l
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405 <!-- Verify trackDb.txt contains the basic fields for a bam -->
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406 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
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yating-l
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407 <assert_contents>
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408 <has_text text="track"/>
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yating-l
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diff changeset
409 <has_text text="longLabel"/>
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diff changeset
410 <has_text text="shortLabel"/>
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diff changeset
411 <has_text text="bigDataUrl"/>
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yating-l
parents: 18
diff changeset
412 <has_text text="type"/>
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yating-l
parents: 18
diff changeset
413 <has_text text="visibility"/>
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yating-l
parents: 18
diff changeset
414 <has_text text="thickDrawItem"/>
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yating-l
parents: 18
diff changeset
415 <has_text text="priority"/>
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yating-l
parents: 18
diff changeset
416 <has_text text="color"/>
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yating-l
parents: 18
diff changeset
417 <has_text text="group"/>
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yating-l
parents: 18
diff changeset
418 </assert_contents>
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yating-l
parents: 18
diff changeset
419 </extra_files>
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yating-l
parents: 18
diff changeset
420 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
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yating-l
parents: 18
diff changeset
421 </output>
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yating-l
parents: 18
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422 </test>
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yating-l
parents: 18
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423
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
424 <!-- Test with Bed Generic -->
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yating-l
parents: 18
diff changeset
425 <test>
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yating-l
parents: 18
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426 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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427 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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428 <repeat name="group">
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yating-l
parents: 18
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429 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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430 <repeat name="format">
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yating-l
parents: 18
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431 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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432 <param name="format_select" value="bed" />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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433 <conditional name="bedChoice">
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yating-l
parents: 18
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434 <param name="bed_select" value="bed_generic"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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435 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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436 <param name="track_color" value="#000000"/>
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yating-l
parents: 18
diff changeset
437 </conditional>
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yating-l
parents: 18
diff changeset
438 </conditional>
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yating-l
parents: 18
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439 </repeat>
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yating-l
parents: 18
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440 </repeat>
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yating-l
parents: 18
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441 <output name="output" file="bed_generic/bed_generic.html">
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yating-l
parents: 18
diff changeset
442 <!-- Verify tracks folder contains bam and bai -->
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yating-l
parents: 18
diff changeset
443 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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444 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
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445 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
446 compare="sim_size"
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yating-l
parents: 18
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447 />
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yating-l
parents: 18
diff changeset
448 </output>
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yating-l
parents: 18
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449 </test>
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yating-l
parents: 18
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450
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yating-l
parents: 18
diff changeset
451 <!-- Test with Bed Simple repeat -->
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yating-l
parents: 18
diff changeset
452 <test>
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yating-l
parents: 18
diff changeset
453 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
454 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
455 <repeat name="group">
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yating-l
parents: 18
diff changeset
456 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
457 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
458 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
459 <param name="format_select" value="bed" />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
460 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
461 <param name="bed_select" value="bed_simple_repeats_option"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
462 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
463 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
464 </conditional>
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yating-l
parents: 18
diff changeset
465 </conditional>
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yating-l
parents: 18
diff changeset
466 </repeat>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
467 </repeat>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
468 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
469 <!-- Verify tracks folder contains bam and bai -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
470 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
471 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
472 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
473 compare="sim_size"
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yating-l
parents: 18
diff changeset
474 />
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yating-l
parents: 18
diff changeset
475 </output>
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yating-l
parents: 18
diff changeset
476 </test>
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yating-l
parents: 18
diff changeset
477
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yating-l
parents: 18
diff changeset
478
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
479 <!-- Test with Psl -->
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yating-l
parents: 18
diff changeset
480 <test>
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yating-l
parents: 18
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481 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
482 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
483 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
484 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
485 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
486 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
487 <param name="format_select" value="psl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
488 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
489 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
490 </conditional>
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yating-l
parents: 18
diff changeset
491 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
492 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
493 <output name="output" file="psl/psl_trackhub.html">
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yating-l
parents: 18
diff changeset
494 <!-- Verify tracks folder contains bam and bai -->
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yating-l
parents: 18
diff changeset
495 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
496 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
497 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
498 compare="sim_size"
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yating-l
parents: 18
diff changeset
499 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
500 <!-- Verify trackDb.txt contains the basic fields for a bam -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
501 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
502 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
503 </test>
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yating-l
parents: 18
diff changeset
504
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
505 <!-- Test with BigWig -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
506 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
507 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
508 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
509 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
510 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
511 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
512 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
513 <param name="format_select" value="bigwig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
514 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
515 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
516 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
517 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
518 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
519 <output name="output" file="bigwig/bigwig.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
520 <!-- Verify tracks folder contains bam and bai -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
521 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
522 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
523 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
524 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
525 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
526 <!-- Verify trackDb.txt contains the basic fields for a bam -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
527 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
528 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
529 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
530
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
531 <!-- Test with GFF3 -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
532 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
533 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
534 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
535 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
536 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
537 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
538 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
539 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
540 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
541 <param name="track_color" value="#000000"/>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
542 </conditional>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
543 </repeat>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
544 </repeat>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
545 <output name="output" file="gff3/gff3_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
546 <!-- Verify tracks folder contains bam and bai -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
547 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
548 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
549 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
550 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
551 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
552 <!-- Verify trackDb.txt contains the basic fields for a bam -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
553 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
554 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
555 </test>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
556
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
557 <!-- Test with GTF -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
558 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
559 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
560 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
561 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
562 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
563 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
564 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
565 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
566 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
567 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
568 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
569 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
570 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
571 <output name="output" file="gtf/gtf_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
572 <!-- Verify tracks folder contains bam and bai -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
573 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
574 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
575 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
576 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
577 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
578 <!-- Verify trackDb.txt contains the basic fields for a bam -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
579 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
580 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
581 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
582
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
583 <!-- Test with one group and multiple tracks -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
584 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
585 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
586 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
587 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
588 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
589 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
590 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
591 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
592 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
593 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
594 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
595 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
596 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
597 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
598 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
599 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
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yating-l
parents: 18
diff changeset
600 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
601 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
602 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
603 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
604 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
605 <!-- verify tracks folder contains bam and bai -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
606 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
607 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
608 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
609 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
610 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
611 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
612 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
613 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
614 compare="sim_size"
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yating-l
parents: 18
diff changeset
615 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
616 <!-- verify trackdb.txt contains the basic fields for a bam -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
617 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
618 </output>
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rmarenco
parents:
diff changeset
619 </test>
20
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yating-l
parents: 18
diff changeset
620
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yating-l
parents: 18
diff changeset
621 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
622 <test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
623 <param name="genome_name" value="Dbia3"/>
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yating-l
parents: 18
diff changeset
624 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
625 <repeat name="group">
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yating-l
parents: 18
diff changeset
626 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
627 <repeat name="format">
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yating-l
parents: 18
diff changeset
628 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
629 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
630 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
631 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
632 </conditional>
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yating-l
parents: 18
diff changeset
633 </repeat>
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yating-l
parents: 18
diff changeset
634 <repeat name="format">
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yating-l
parents: 18
diff changeset
635 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
636 <param name="format_select" value="bed"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
637 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
638 <param name="bed_select" value="bed_generic"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
639 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
640 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
641 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
642 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
643 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
644 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
645 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
646 <param name="format_select" value="bed"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
647 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
648 <param name="bed_select" value="bed_simple_repeats_option"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
649 <param name="BED_simple_repeats" ftype="bed"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
650 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
651 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
652 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
653 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
654 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
655 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
656 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
657 <param name="format_select" value="psl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
658 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
659 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
660 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
661 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
662 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
663 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
664 <param name="format_select" value="bigwig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
665 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
666 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
667 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
668 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
669 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
670 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
671 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
672 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
673 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
674 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
675 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
676 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
677 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
678 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
679 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
680 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
681 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
682 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
683 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
684 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
685 <!-- verify tracks folder contains all the files -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
686 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
687 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
688 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
689 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
690 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
691 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
692 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
693 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
694 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
695 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
696 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
697 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
698 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
699 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
700 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
701 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
702 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
703 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
704 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
705 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
706 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
707 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
708 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
709 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
710 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
711 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
712 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
713 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
714 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
715 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
716 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
717 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
718 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
719 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
720 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
721 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
722 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
723 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
724 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
725 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
726 <!-- verify trackdb.txt contains the basic fields for a bam -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
727 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
728 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
729 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
730
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
731 <!-- Test with two groups and no tracks -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
732 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
733 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
734 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
735 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
736 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
737 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
738 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
739 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
740 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
741 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
742 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
743 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
744 <!-- Email could be different, but we need to ensure we still have the email line -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
745 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
746 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
747 <has_text text="email"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
748 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
749 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
750 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
751 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
752 <extra_files type="file" name="myHub/Dbia3/description.html"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
753 value="two_groups_no_track/myHub/Dbia3/description.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
754 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
755 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
756
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
757 <!-- Test with two groups and one track in first -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
758 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
759 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
760 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
761 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
762 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
763 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
764 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
765 <param name="format_select" value="bigwig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
766 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
767 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
768 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
769 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
770 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
771 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
772 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
773 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
774 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
775 <!-- Check myHub structure -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
776 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
777 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
778 <!-- Email could be different, but we need to ensure we still have the email line -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
779 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
780 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
781 <has_text text="email"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
782 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
783 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
784 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
785 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
786 <extra_files type="file" name="myHub/Dbia3/description.html"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
787 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
788
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
789 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
790 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
791 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
792 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
793 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
794 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
795
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
796 <!-- Check the groups.txt exists and is properly populated -->
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
797 </output>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
798 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
799
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
800 <!-- Test with two groups and one track in both -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
801 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
802 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
803 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
804 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
805 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
806 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
807 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
808 <param name="format_select" value="bigwig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
809 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
810 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
811 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
812 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
813 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
814 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
815 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
816 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
817 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
818 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
819 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
820 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
821 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
822 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
823 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
824 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
825 <!-- Check myHub structure -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
826 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
827 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
828 <!-- Email could be different, but we need to ensure we still have the email line -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
829 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
830 lines_diff="2">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
831 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
832 <has_text text="email"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
833 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
834 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
835 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
836 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
837 <extra_files type="file" name="myHub/Dbia3/description.html"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
838 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
839
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
840 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
841 <!-- First group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
842 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
843 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
844 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
845 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
846 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
847
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
848 <!-- Second group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
849 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
850 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
851 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
852 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
853 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
854 <!-- Check the groups.txt exists and is properly populated -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
855 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
856 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
857
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
858 <!-- Test with two groups and multiple tracks in both -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
859 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
860 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
861 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
862 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
863 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
864 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
865 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
866 <param name="format_select" value="bigwig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
867 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
868 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
869 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
870 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
871 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
872 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
873 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
874 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
875 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
876 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
877 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
878 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
879 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
880 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
881 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
882 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
883 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
884 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
885 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
886 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
887 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
888 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
889 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
890 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
891 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
892 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
893 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
894 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
895 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
896 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
897 <!-- Check myHub structure -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
898 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
899 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
900 <!-- Email could be different, but we need to ensure we still have the email line -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
901 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
902 lines_diff="2">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
903 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
904 <has_text text="email"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
905 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
906 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
907 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
908 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
909 <extra_files type="file" name="myHub/Dbia3/description.html"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
910 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
911
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
912 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
913 <!-- First group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
914 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
915 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
916 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
917 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
918 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
919 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
920 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
921 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
922 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
923 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
924 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
925 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
926 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
927 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
928 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
929
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
930 <!-- Second group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
931 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
932 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
933 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
934 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
935 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
936 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
937 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
938 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
939 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
940 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
941 <!-- Check the groups.txt exists and is properly populated -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
942 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
943 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
944
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
945 <!-- Test default color in a track -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
946 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
947 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
948 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
949 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
950 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
951 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
952 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
953 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
954 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
955 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
956 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
957 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
958 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
959 <output name="output" file="default_color/default_color_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
960 <!-- Verify trackDb.txt contains the color 0,0,0 -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
961 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
962 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
963 <has_text text="color 0,0,0"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
964 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
965 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
966
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
967 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
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parents: 18
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968 </output>
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969 </test>
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970
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971 <!-- Test changed color in a track -->
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972 <test>
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973 <param name="genome_name" value="Dbia3"/>
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974 <param name="fasta_file" value="common/dbia3.fa"/>
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975 <repeat name="group">
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976 <param name="group_name" value="Default group"/>
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977 <repeat name="format">
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978 <conditional name="formatChoice">
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979 <param name="format_select" value="bam"/>
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980 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
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981 <param name="track_color" value="#8064a2"/>
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982 </conditional>
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983 </repeat>
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984 </repeat>
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985 <output name="output" file="changed_color/changed_color_trackhub.html">
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parents: 18
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986 <!-- Verify trackDb.txt contains the color 128,100,162 -->
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987 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
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988 <assert_contents>
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989 <has_text text="color 128,100,162"/>
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990 </assert_contents>
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991 </extra_files>
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992
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993 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
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994 </output>
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995 </test>
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996
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997 <!-- Test for StringTie Chromosome end coordinates -->
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998 <test>
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999 <param name="genome_name" value="Dbia3"/>
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1000 <param name="fasta_file" value="common/dbia3.fa"/>
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1001 <repeat name="group">
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1002 <param name="group_name" value="Default group"/>
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1003 <repeat name="format">
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1004 <conditional name="formatChoice">
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1005 <param name="format_select" value="gtf"/>
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1006 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
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1007 <param name="track_color" value="#000000"/>
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1008 </conditional>
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1009 </repeat>
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1010 </repeat>
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1011 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
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1012 <extra_files type="file"
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1013 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
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1014 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
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1015 compare="sim_size"
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1016 />
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1017
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1018 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
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1019 </output>
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1020 </test>
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1021
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1022 <!-- Test for big files? -->
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1023
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1024 <!-- Find tests that should fail -->
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1025
0
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1026 </tests>
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1027
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1028 <help>
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1029 This Galaxy tool permits to prepare your files to be ready for
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1030 Assembly Hub visualization.
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1031 </help>
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1032 </tool>