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annotate hubArchiveCreator.xml @ 3:fa990284327b draft default tip

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Mon, 30 Oct 2017 11:58:31 -0400
parents 85195e0d4b71
children
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0">
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2 <description>
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3 This Galaxy tool permits to prepare your files to be ready for
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4 Assembly Hub visualization.
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5 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
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10 <requirements>
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11 <requirement type="package" version="340">ucsc_hac</requirement>
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12 <requirement type="package" version="1.2">samtools</requirement>
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13 <requirement type="package" version="340">ucsc_bigwig</requirement>
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14 <requirement type="package" version="340">ucsc_bigbed</requirement>
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15 </requirements>
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17 <stdio>
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18 <regex match="^pass1"
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19 source="stderr"
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20 level="log"
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21 description="bedToBigBed"/>
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22 <!-- TODO: Add the case pass1 and 0 chroms -->
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23 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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24 </stdio>
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26 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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27 <command detect_errors="exit_code"><![CDATA[
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28 mkdir -p $output.extra_files_path;
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29
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30 ## Dump the tool parameters into a JSON file
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31 python $json_file parameters.json;
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33 python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output;
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36 ]]></command>
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37 <configfiles>
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38 <configfile name="json_file">
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39 import json
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40 import sys
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41
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42 file_path = sys.argv[1]
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43 #set global $data_parameter_dict = {}
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44
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45 ## Ask the user to enter the genome name
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46 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
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47
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48 ## Function to retrieve the data of the inputs
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49 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
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50 #set false_path = str($input_to_prepare)
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51 #set $data_dict = {"false_path": $false_path}
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52
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53 #set name = str($input_to_prepare.name)
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54 #silent $data_dict.update({"name": $name})
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55 #silent $data_dict.update($extra_data_dict)
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56 ## Add the ordering by taking the tool form indexes
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57 #silent $data_dict.update({"order_index": $order_index})
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58
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59 #if $datatype in $data_parameter_dict
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60 #silent $data_parameter_dict[$datatype].append($data_dict)
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61 #else
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62 #set array_inputs = []
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63 #silent $array_inputs.append($data_dict)
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64 #silent $data_parameter_dict.update({$datatype: $array_inputs})
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65 #end if
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66 #end def
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67
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68 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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69
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70 #set temp_max_digit = 0
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71
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72 #for $g in $group
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73 #if len($g.format) > $temp_max_digit
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74 #silent temp_max_digit = len($g.format)
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75 #end if
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76 #end for
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77
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79 #set nb_digits_max_track = len(str($temp_max_digit))
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80
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81 ## END Get the number of digits
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82
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83 #for $i_g, $g in enumerate( $group )
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84 #for $i, $f in enumerate( $g.format )
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85 ## Create the order index using index_group+1 concatenated with index_track
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86 #set index_group_final = str($i_g + 1)
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87 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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88
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89 ## For each format, we have a few mandatory fields we store in a dict
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90 #set track_color = str($f.formatChoice.track_color)
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91 #set group_name = str($g.group_name)
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92 #set longLabel = str($f.formatChoice.longLabel)
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93 #set extra_data_dict = {"track_color": $track_color,
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94 "group_name": $group_name,
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95 "long_label": $longLabel}
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96
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97 #if $f.formatChoice.format_select == "bam"
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98 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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99
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100 ## Add Bam format specific fields
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101 #silent $extra_data_dict.update({"index": $bam_index})
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102
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103 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
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104 #end if
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105 #if $f.formatChoice.format_select == "bed"
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106 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
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107 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final,
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108 $extra_data_dict)
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109 #end if
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110 #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand"
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111 #silent $prepare_json("CytoBand", $f.formatChoice.bedChoice.BED_cytoBand, $index_track_final,
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112 $extra_data_dict)
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113 #end if
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114 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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115 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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116 $extra_data_dict)
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117 #end if
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118 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
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119 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
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120 $extra_data_dict)
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121 #end if
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122 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
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123 #set database = str($f.formatChoice.bedChoice.database)
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124 #silent $extra_data_dict.update({"database": $database})
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125 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
3
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126 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix)
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127 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
1
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128 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
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129 #end if
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130 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
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131 $extra_data_dict)
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132 #end if
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133 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
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134 #set database = str($f.formatChoice.bedChoice.database)
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135 #silent $extra_data_dict.update({"database": $database})
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136 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
3
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137 #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix)
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138 #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
1
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139 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
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140 #end if
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141 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
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142 $extra_data_dict)
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143 #end if
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144 #end if
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145 #if $f.formatChoice.format_select == "psl"
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146 #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final,
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147 $extra_data_dict)
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148 #end if
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149 #if $f.formatChoice.format_select == "bigwig"
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150 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
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151 $extra_data_dict)
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152 #end if
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153 #if $f.formatChoice.format_select == "bigbed"
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154 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
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155 #set ix_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ix)
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156 #set ixx_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
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157 #set trix_id = str($f.formatChoice.add_trix_index.add_trix_file.trix_id)
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158 #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
1
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159 #end if
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160 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
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161 $extra_data_dict)
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162 #end if
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163 #if $f.formatChoice.format_select == "gff3"
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164 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
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165 $extra_data_dict)
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166 #end if
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167 #if $f.formatChoice.format_select == "gtf"
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168 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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169 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
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170 $extra_data_dict)
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171 #end if
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172 #end for
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173 #end for
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174
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175 ## We combine the fasta file dataset name with his false path in a JSON object
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176 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
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177 $data_parameter_dict.update({"fasta": $fasta_json})
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178
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179 ## Retrieve the user email
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180 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
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181
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182 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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183
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184 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
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185
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186 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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187
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188 with open(file_path, 'w') as f:
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189 json.dump($data_parameter_dict, f)
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190
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191 </configfile>
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192 </configfiles>
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193
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194 <inputs>
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195 <param
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196 name="genome_name"
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197 type="text"
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198 size="30"
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199 value="unknown"
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200 label="UCSC Genome Browser assembly ID"
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201 />
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202 <param
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203 format="fasta"
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204 name="fasta_file"
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205 type="data"
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206 label="Reference genome"
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207 />
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208 <repeat name="group" title="New group">
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209 <param type="text" name="group_name" label="Group name" value="Default group"/>
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210 <repeat name="format" title="New track">
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211 <conditional name="formatChoice">
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212 <param name="format_select" type="select" label="Format">
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213 <option value="bam" selected="true">BAM</option>
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214 <option value="bed">BED</option>
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215 <option value="psl">PSL</option>
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216 <option value="bigwig">BIGWIG</option>
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217 <option value="bigbed">BIGBED</option>
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218 <option value="gff3">GFF3</option>
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219 <option value="gtf">GTF</option>
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220 </param>
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221
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222 <when value="bam">
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223 <param
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224 format="bam"
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225 name="BAM"
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226 type="data"
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227 label="BAM File"
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228 />
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229 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
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230 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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231 <param name="track_color" type="color" label="Track color" value="#000000">
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232 <sanitizer>
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233 <valid initial="string.letters,string.digits">
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234 <add value="#"/>
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235 </valid>
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236 </sanitizer>
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237 </param>
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238 </when>
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239 <when value="bed">
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240 <conditional name="bedChoice">
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241 <param name="bed_select" type="select" label="Bed Choice">
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242 <option value="bed_generic" selected="true">BED Generic (bed4)</option>
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243 <option value="bed_cytoBand">cytoBand Track (bed4+1)</option>
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244 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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245 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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246 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
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247 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
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248 </param>
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249 <when value="bed_generic">
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250 <param
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251 format="bed"
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252 name="BED"
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253 type="data"
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254 label="Generic Bed File Choice"
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255 />
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256
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257 </when>
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258 <when value="bed_cytoBand">
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259 <param
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260 format="bed"
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261 name="BED_cytoBand"
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262 type="data"
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263 label="cytoBand Track (Bed4)"
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264 />
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265 </when>
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266 <when value="bed_simple_repeats_option">
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267 <param
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268 format="bed"
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269 name="BED_simple_repeats"
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270 type="data"
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271 label="Bed Simple Repeats (Bed4+12) File"
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272 />
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273 </when>
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274 <when value="bed_splice_junctions_option">
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275 <param
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276 format="bed"
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277 name="BED_splice_junctions"
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278 type="data"
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279 label="Bed Splice Junctions (Bed12+1) File"
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280 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
281 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
282 <when value="bed_blast_alignment_option">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
283 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
284 format="bed"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
285 name="BED_blast_alignment"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
286 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
287 label="Bed Blast Alignments (Bed12+12) File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
288 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
289 <param name="database" type="select" label="Protein database">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
290 <option value="NCBI" selected="true">NCBI</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
291 <option value="UniProt">UniProt</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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292 <option value="FlyBase">FlyBase</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
293 <option value="Others">Others</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
294 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
295 <expand macro="add_trix_file"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
296 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
297 <when value="bed_blat_alignment_option">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
298 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
299 format="bed"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
300 name="BED_blat_alignment"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
301 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
302 label="Bed BLAT Alignments (bigPsl) File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
303 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
304 <param name="database" type="select" label="mRNA database">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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305 <option value="NCBI" selected="true">NCBI</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
306 <option value="Others">Others</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
307 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
308 <expand macro="add_trix_file"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
309 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
310 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
311 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
312 <param name="track_color" type="color" label="Track color" value="#000000">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
313 <sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
314 <valid initial="string.letters,string.digits">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
315 <add value="#"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
316 </valid>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
317 </sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
318 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
319 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
320 <when value="psl">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
321 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
322 format="psl"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
323 name="PSL"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
324 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
325 label="PSL File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
326 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
327 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
328 <param name="track_color" type="color" label="Track color" value="#000000">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
329 <sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
330 <valid initial="string.letters,string.digits">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
331 <add value="#"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
332 </valid>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
333 </sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
334 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
335 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
336 <when value="bigwig">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
337 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
338 format="bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
339 name="BIGWIG"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
340 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
341 label="BIGWIG File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
342 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
343 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
344 <param name="track_color" type="color" label="Track color" value="#000000">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
345 <sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
346 <valid initial="string.letters,string.digits">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
347 <add value="#"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
348 </valid>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
349 </sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
350 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
351 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
352 <when value="bigbed">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
353 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
354 format="bigbed"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
355 name="BIGBED"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
356 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
357 label="BIGBED File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
358 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
359 <expand macro="add_trix_file">
3
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 1
diff changeset
360 <param
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 1
diff changeset
361 name="trix_id"
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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parents: 1
diff changeset
362 value="name"
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 1
diff changeset
363 type="text"
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 1
diff changeset
364 size="30"
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 1
diff changeset
365 label="Specify Trix identifier"
fa990284327b planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 1
diff changeset
366 />
1
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
367 </expand>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
368 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
369 <param name="track_color" type="color" label="Track color" value="#000000">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
370 <sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
371 <valid initial="string.letters,string.digits">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
372 <add value="#"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
373 </valid>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
374 </sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
375 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
376 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
377 <when value="gff3">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
378 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
379 format="gff3"
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diff changeset
380 name="GFF3"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
381 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
382 label="GFF3 File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
383 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
384 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
385 <param name="track_color" type="color" label="Track color" value="#000000">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
386 <sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
387 <valid initial="string.letters,string.digits">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
388 <add value="#"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
389 </valid>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
390 </sanitizer>
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diff changeset
391 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
392 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
393 <when value="gtf">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
394 <param
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
395 format="gtf"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
396 name="GTF"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
397 type="data"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
398 label="GTF File"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
399 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
400 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
401 <param name="track_color" type="color" label="Track color" value="#000000">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
402 <sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
403 <valid initial="string.letters,string.digits">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
404 <add value="#"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
405 </valid>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
406 </sanitizer>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
407 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
408 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
409 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
410 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
411 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
412 <conditional name="advanced_options">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
413 <param name="advanced_options_selector" type="select" label="Advanced options">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
414 <option value="off" selected="true">Hide advanced options</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
415 <option value="on">Display advanced options</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
416 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
417 <!-- TODO: Avoid redundancy here -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
418 <when value="on">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
419 <param name="debug_mode" type="select" label="Activate debug mode">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
420 <option value="false" selected="true">No</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
421 <option value="true">Yes</option>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
422 <help>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
423 Use this option if you are a G-OnRamp developer
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
424 </help>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
425 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
426 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
427 <when value="off">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
428 <param name="debug_mode" type="hidden"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
429 value="false">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
430 </param>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
431 </when>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
432 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
433 </inputs>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
434
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
435 <outputs>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
436 <data format="trackhub" name="output"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
437 </outputs>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
438
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
439 <tests>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
440 <!-- Test with only the fasta file -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
441 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
442 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
443 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
444 <output name="output" file="only_genome/only_genome.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
445 <!-- Use macro to check the whole common structure without repeated code -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
446 <expand macro="verify_hub_structure_no_track" test="only_genome" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
447 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
448 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
449
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
450 <!-- Test with Bam -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
451 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
452 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
453 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
454 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
455 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
456 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
457 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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diff changeset
458 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
459 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
460 <param name="longLabel" value="HISAT sequence alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
461 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
462 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
463 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
464 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
465 <output name="output" file="bam/bam.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
466 <!-- Verify tracks folder contains bam and bai -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
467 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
468 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
469 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
470 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
471 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
472 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
473 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
474 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
475 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
476 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
477 <!-- Use macro to check the whole common structure without repeated code -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
478 <expand macro="verify_hub_structure" test="bam" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
479 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
480 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
481
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
482 <!-- Test with Bed Generic -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
483 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
484 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
485 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
486 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
487 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
488 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
489 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
490 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
491 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
492 <param name="bed_select" value="bed_generic"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
493 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
494 <param name="longLabel" value="TBLASTN alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
495 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
496 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
497 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
498 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
499 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
500 <output name="output" file="bed_generic/bed_generic.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
501 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
502 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
503 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
504 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
505 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
506 <expand macro="verify_hub_structure" test="bed_generic" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
507 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
508 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
509
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
510 <!-- Test with Bed Simple repeat -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
511 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
512 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
513 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
514 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
515 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
516 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
517 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
518 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
519 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
520 <param name="bed_select" value="bed_simple_repeats_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
521 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
522 <param name="longLabel" value="Simple repeat" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
523 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
524 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
525 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
526 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
527 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
528 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
529 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
530 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
531 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
532 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
533 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
534 <expand macro="verify_hub_structure" test="bed_simple_repeats" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
535 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
536 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
537
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
538 <!-- Test with Psl -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
539 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
540 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
541 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
542 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
543 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
544 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
545 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
546 <param name="format_select" value="psl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
547 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
548 <param name="longLabel" value="BLAST Alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
549 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
550 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
551 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
552 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
553 <output name="output" file="psl/psl_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
554 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
555 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
556 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
557 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
558 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
559 <expand macro="verify_hub_structure" test="psl" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
560 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
561 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
562
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
563 <!-- Test with BigWig -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
564 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
565 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
566 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
567 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
568 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
569 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
570 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
571 <param name="format_select" value="bigwig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
572 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
573 <param name="longLabel" value="RNA-Seq Coverage" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
574 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
575 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
576 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
577 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
578 <output name="output" file="bigwig/bigwig.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
579 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
580 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
581 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
582 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
583 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
584 <expand macro="verify_hub_structure" test="bigwig" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
585 <!-- check additional trackDb settings for BigWig -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
586 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
587 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
588 <has_text text="autoScale"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
589 <has_text text="maxHeightPixels"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
590 <has_text text="windowingFunction"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
591 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
592 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
593 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
594 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
595
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
596 <!-- Test with GFF3 -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
597 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
598 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
599 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
600 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
601 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
602 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
603 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
604 <param name="format_select" value="gff3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
605 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
606 <param name="longLabel" value="Augustus" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
607 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
608 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
609 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
610 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
611 <output name="output" file="gff3/gff3_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
612 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
613 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
614 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
615 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
616 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
617 <expand macro="verify_hub_structure" test="gff3" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
618 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
619 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
620
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
621 <!-- Test with GTF -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
622 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
623 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
624 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
625 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
626 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
627 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
628 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
629 <param name="format_select" value="gtf"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
630 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
631 <param name="longLabel" value="StringTie transcripts" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
632 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
633 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
634 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
635 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
636 <output name="output" file="gtf/gtf_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
637 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
638 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
639 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
640 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
641 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
642 <expand macro="verify_hub_structure" test="gtf" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
643 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
644 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
645
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
646 <!-- Test with BLAT Alignment -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
647 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
648 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
649 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
650 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
651 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
652 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
653 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
654 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
655 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
656 <param name="bed_select" value="bed_blat_alignment_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
657 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
658 <param name="longLabel" value="BLAT alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
659 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
660 <param name="database" value="NCBI" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
661 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
662 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
663 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
664 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
665 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
666 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
667 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
668 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
669 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
670 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
671 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
672 <!-- check additional trackDb settings for BLAT -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
673 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
674 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
675 <has_text text="searchIndex"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
676 <has_text text="url"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
677 <has_text text="urlLabel"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
678 <has_text text="iframeUrl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
679 <has_text text="iframeOptions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
680 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
681 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
682 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
683 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
684
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
685 <!-- Test with BLAST Alignment -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
686 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
687 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
688 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
689 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
690 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
691 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
692 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
693 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
694 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
695 <param name="bed_select" value="bed_blast_alignment_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
696 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
697 <param name="longLabel" value="BLAST alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
698 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
699 <param name="database" value="NCBI" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
700 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
701 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
702 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
703 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
704 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
705 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
706 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
707 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
708 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
709 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
710 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
711 <!-- check additional trackDb settings for BLAST -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
712 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
713 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
714 <has_text text="searchIndex"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
715 <has_text text="url"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
716 <has_text text="urlLabel"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
717 <has_text text="iframeUrl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
718 <has_text text="iframeOptions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
719 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
720 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
721 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
722 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
723
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
724 <!-- Test with Regtools Splice Junctions -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
725 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
726 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
727 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
728 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
729 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
730 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
731 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
732 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
733 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
734 <param name="bed_select" value="bed_splice_junctions_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
735 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
736 <param name="longLabel" value="Splice junctions" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
737 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
738 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
739 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
740 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
741 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
742 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
743 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
744 name="myHub/Dbia3/tracks/regtools_junctions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
745 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
746 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
747 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
748 <expand macro="verify_hub_structure" test="bed_splice_junctions" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
749 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
750 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
751
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
752 <!-- Test with Cytoband -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
753 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
754 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
755 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
756 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
757 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
758 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
759 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
760 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
761 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
762 <param name="bed_select" value="bed_cytoBand"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
763 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
764 <param name="longLabel" value="Cytoband" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
765 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
766 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
767 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
768 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
769 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
770 <output name="output" file="bed_cytoband/cytoband_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
771 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
772 name="myHub/Dbia3/tracks/Cytoband.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
773 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
774 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
775 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
776 <expand macro="verify_hub_structure" test="bed_cytoband" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
777 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
778 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
779 <has_text text="track cytoBandIdeo"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
780 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
781 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
782 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
783 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
784
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
785 <!-- Test with bigBed -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
786 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
787 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
788 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
789 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
790 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
791 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
792 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
793 <param name="format_select" value="bigbed"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
794 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
795 <param name="longLabel" value="bigBed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
796 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
797 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
798 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
799 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
800 <output name="output" file="big_bed/bigbed_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
801 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
802 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
803 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
804 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
805 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
806 <expand macro="verify_hub_structure" test="big_bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
807 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
808 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
809
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
810 <!-- Test with one group and multiple tracks -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
811 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
812 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
813 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
814 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
815 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
816 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
817 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
818 <param name="format_select" value="gtf"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
819 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
820 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
821 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
822 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
823 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
824 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
825 <param name="format_select" value="gff3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
826 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
827 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
828 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
829 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
830 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
831 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
832 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
833 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
834 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
835 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
836 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
837 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
838 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
839 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
840 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
841 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
842 <expand macro="verify_hub_structure" test="gtf_gff" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
843 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
844 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
845
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
846 <!-- Test with one group and all the supported datatypes -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
847 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
848 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
849 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
850 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
851 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
852 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
853 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
854 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
855 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
856 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
857 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
858 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
859 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
860 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
861 <param name="format_select" value="bed"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
862 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
863 <param name="bed_select" value="bed_generic"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
864 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
865 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
866 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
867 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
868 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
869 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
870 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
871 <param name="format_select" value="bed"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
872 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
873 <param name="bed_select" value="bed_simple_repeats_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
874 <param name="BED_simple_repeats" ftype="bed"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
875 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
876 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
877 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
878 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
879 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
880 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
881 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
882 <param name="format_select" value="psl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
883 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
884 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
885 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
886 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
887 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
888 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
889 <param name="format_select" value="bigwig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
890 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
891 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
892 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
893 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
894 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
895 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
896 <param name="format_select" value="gff3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
897 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
898 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
899 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
900 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
901 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
902 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
903 <param name="format_select" value="gtf"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
904 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
905 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
906 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
907 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
908 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
909 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
910 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
911 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
912 <param name="bed_select" value="bed_cytoBand"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
913 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
914 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
915 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
916 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
917 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
918 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
919 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
920 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
921 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
922 <param name="bed_select" value="bed_splice_junctions_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
923 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
924 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
925 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
926 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
927 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
928 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
929 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
930 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
931 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
932 <param name="bed_select" value="bed_blast_alignment_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
933 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
934 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
935 <param name="database" value="NCBI" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
936 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
937 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
938 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
939 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
940 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
941 <param name="format_select" value="bed" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
942 <conditional name="bedChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
943 <param name="bed_select" value="bed_blat_alignment_option"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
944 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
945 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
946 <param name="database" value="NCBI" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
947 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
948 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
949 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
950 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
951 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
952 <!-- verify tracks folder contains all the files -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
953 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
954 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
955 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
956 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
957 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
958 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
959 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
960 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
961 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
962 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
963 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
964 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
965 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
966 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
967 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
968 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
969 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
970 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
971 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
972 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
973 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
974 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
975 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
976 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
977 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
978 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
979 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
980 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
981 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
982 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
983 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
984 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
985 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
986 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
987 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
988 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
989 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
990 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
991 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
992 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
993 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
994 name="myHub/Dbia3/tracks/Cytoband.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
995 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
996 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
997 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
998 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
999 name="myHub/Dbia3/tracks/regtools_junctions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1000 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1001 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1002 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1003 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1004 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1005 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1006 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1007 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1008 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1009 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1010 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1011 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1012 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1013 <expand macro="verify_hub_structure" test="all_datatypes" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1014 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1015 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1016
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1017 <!-- Test with two groups and no tracks -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1018 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1019 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1020 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1021 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1022 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1023 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1024 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1025 <param name="group_name" value="Other group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1026 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1027 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1028 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1029 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1030 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1031
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1032 <!-- Test with two groups and one track in first -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1033 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1034 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1035 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1036 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1037 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1038 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1039 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1040 <param name="format_select" value="bigwig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1041 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1042 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1043 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1044 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1045 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1046 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1047 <param name="group_name" value="Other group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1048 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1049 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1050 <!-- Check tracks exist -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1051 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1052 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1053 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1054 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1055 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1056 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1057 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1058 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1059
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1060 <!-- Test with two groups and one track in both -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1061 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1062 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1063 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1064 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1065 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1066 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1067 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1068 <param name="format_select" value="bigwig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1069 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1070 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1071 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1072 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1073 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1074 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1075 <param name="group_name" value="Other group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1076 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1077 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1078 <param name="format_select" value="gtf"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1079 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1080 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1081 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1082 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1083 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1084 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1085 <!-- Check tracks exist -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1086 <!-- First group -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1087 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1088 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1089 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1090 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1091 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1092
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1093 <!-- Second group -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1094 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1095 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1096 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1097 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1098 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1099 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1100 <!-- Check the groups.txt exists and is properly populated -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1101 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1102 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1103
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1104 <!-- Test with two groups and multiple tracks in both -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1105 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1106 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1107 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1108 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1109 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1110 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1111 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1112 <param name="format_select" value="bigwig"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1113 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1114 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1115 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1116 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1117 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1118 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1119 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1120 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1121 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1122 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1123 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1124 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1125 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1126 <param name="group_name" value="Other group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1127 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1128 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1129 <param name="format_select" value="gtf"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1130 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1131 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1132 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1133 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1134 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1135 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1136 <param name="format_select" value="gff3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1137 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1138 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1139 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1140 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1141 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1142 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1143 <!-- Check tracks exist -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1144 <!-- First group -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1145 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1146 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1147 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1148 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1149 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1150 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1151 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1152 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1153 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1154 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1155 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1156 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1157 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1158 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1159 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1160
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1161 <!-- Second group -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1162 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1163 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1164 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1165 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1166 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1167 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1168 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1169 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1170 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1171 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1172 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1173 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1174 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1175
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1176 <!-- Test default color in a track -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1177 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1178 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1179 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1180 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1181 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1182 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1183 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1184 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1185 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1186 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1187 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1188 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1189 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1190 <output name="output" file="default_color/default_color_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1191 <expand macro="verify_hub_structure" test="default_color" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1192 <!-- Verify trackDb.txt contains the color 0,0,0 -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1193 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1194 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1195 <has_text text="color 0,0,0"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1196 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1197 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1198
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1199 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1200 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1201 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1202
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1203 <!-- Test changed color in a track -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1204 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1205 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1206 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1207 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1208 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1209 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1210 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1211 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1212 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1213 <param name="track_color" value="#8064a2"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1214 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1215 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1216 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1217 <output name="output" file="changed_color/changed_color_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1218 <expand macro="verify_hub_structure" test="changed_color" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1219 <!-- Verify trackDb.txt contains the color 128,100,162 -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1220 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1221 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1222 <has_text text="color 128,100,162"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1223 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1224 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1225
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1226 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1227 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1228 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1229
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1230 <!-- Test for StringTie Chromosome end coordinates -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1231 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1232 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1233 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1234 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1235 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1236 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1237 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1238 <param name="format_select" value="gtf"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1239 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1240 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1241 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1242 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1243 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1244 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1245 <extra_files type="file"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1246 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1247 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1248 compare="sim_size"
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1249 />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1250 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1251
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1252 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1253 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1254 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1255
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1256 <!-- Test default label in a track -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1257 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1258 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1259 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1260 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1261 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1262 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1263 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1264 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1265 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1266 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1267 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1268 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1269 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1270 <output name="output" file="default_color/default_color_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1271 <expand macro="verify_hub_structure" test="default_color" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1272 <!-- Verify trackDb.txt contains default label -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1273 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1274 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1275 <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1276 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1277 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1278
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1279 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1280 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1281 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1282
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1283 <!-- Test customized label in a track -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1284 <test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1285 <param name="genome_name" value="Dbia3"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1286 <param name="fasta_file" value="common/dbia3.fa"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1287 <repeat name="group">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1288 <param name="group_name" value="Default group"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1289 <repeat name="format">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1290 <conditional name="formatChoice">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1291 <param name="format_select" value="bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1292 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1293 <param name="longLabel" value="HISAT sequence alignment" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1294 <param name="track_color" value="#000000"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1295 </conditional>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1296 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1297 </repeat>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1298 <output name="output" file="changed_label/changed_label_trackhub.html">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1299 <expand macro="verify_hub_structure" test="changed_label" />
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1300 <!-- Verify trackDb.txt contains the customized label -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1301 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1302 <assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1303 <has_text text="longLabel HISAT sequence alignment"/>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1304 </assert_contents>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1305 </extra_files>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1306
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1307 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1308 </output>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1309 </test>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1310
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1311
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diff changeset
1312
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1313
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1314 <!-- Test for big files? -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1315
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1316 <!-- Find tests that should fail -->
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1317
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1318 </tests>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
1319
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parents:
diff changeset
1320 <help>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff changeset
1321 This Galaxy tool permits to prepare your files to be ready for
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1322 Assembly Hub visualization.
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1323 </help>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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diff changeset
1324
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parents:
diff changeset
1325 <citations>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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parents:
diff changeset
1326 <citation type="doi">10.7490/f1000research.1112719.1</citation>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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1327 </citations>
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
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1328 </tool>