Mercurial > repos > rmarenco > hubarchivecreator

annotate hubArchiveCreator.xml @ 30:e7c4be523cb7 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 2f1b3cc8c9cb463e460f7f79efe99ed472700ecf
author yating-l
date Tue, 19 Jun 2018 13:02:32 -0400
parents 7e8a8b732db3
children 9c5d82d3c87e
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.2">
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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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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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16
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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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25
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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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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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42 file_path = sys.argv[1]
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43 #set global $data_parameter_dict = {}
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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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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": $false_path}
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53 #set name = str($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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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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68 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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70 #set temp_max_digit = 0
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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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79 #set nb_digits_max_track = len(str($temp_max_digit))
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81 ## END Get the number of digits
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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($nb_digits_max_track)
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89 ## For each format, we have a few mandatory fields we store in a dict
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90 #set track_color = str($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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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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100 ## Add Bam format specific fields
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101 #silent $extra_data_dict.update({"index": $bam_index})
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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"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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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,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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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,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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112 $extra_data_dict)
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parents: 28
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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,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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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"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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119 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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120 $extra_data_dict)
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121 #end if
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122 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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123 #set database = str($f.formatChoice.bedChoice.database)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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124 #silent $extra_data_dict.update({"database": $database})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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125 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
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126 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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127 #if $i.element_identifier.endswith("ix")
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128 #$extra_data_dict.update({"index_ix": str($i)})
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129 #elif $i.element_identifier.endswith("ixx")
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130 #$extra_data_dict.update({"index_ixx": str($i)})
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131 #end if
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132 #end for
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133 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
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134 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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135 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
0
0f3bc17e5ede Uploaded
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136 #end if
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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137 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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138 $extra_data_dict)
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139 #end if
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140 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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141 #set database = str($f.formatChoice.bedChoice.database)
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142 #silent $extra_data_dict.update({"database": $database})
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143 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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144 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
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145 #if $i.element_identifier.endswith("ix")
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146 #$extra_data_dict.update({"index_ix": str($i)})
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147 #elif $i.element_identifier.endswith("ixx")
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148 #$extra_data_dict.update({"index_ixx": str($i)})
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149 #end if
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150 #end for
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151 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
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152 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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153 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
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154 #end if
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155 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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156 $extra_data_dict)
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157 #end if
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158 #end if
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159 #if $f.formatChoice.format_select == "psl"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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160 #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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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 == "bigwig"
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164 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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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 == "bigbed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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168 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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169 ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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170 ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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171 #for i in $f.formatChoice.add_trix_index.trix_index
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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172 #if $i.element_identifier.endswith("ix")
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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173 #$extra_data_dict.update({"index_ix": str($i)})
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174 #elif $i.element_identifier.endswith("ixx")
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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175 #$extra_data_dict.update({"index_ixx": str($i)})
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176 #end if
29
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177 #end for
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178 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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179 ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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180 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
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181 #end if
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182 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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183 $extra_data_dict)
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184 #end if
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185 #if $f.formatChoice.format_select == "gff3"
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186 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
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187 $extra_data_dict)
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188 #end if
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189 #if $f.formatChoice.format_select == "gtf"
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190 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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191 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
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192 $extra_data_dict)
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193 #end if
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194 #end for
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195 #end for
0
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196
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197 ## We combine the fasta file dataset name with his false path in a JSON object
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198 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
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199 $data_parameter_dict.update({"fasta": $fasta_json})
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200
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201 ## Retrieve the user email
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202 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
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203
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204 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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205
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206 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
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207
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208 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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209
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210 with open(file_path, 'w') as f:
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211 json.dump($data_parameter_dict, f)
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212
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213 </configfile>
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214 </configfiles>
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215
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216 <inputs>
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217 <param
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218 name="genome_name"
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219 type="text"
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220 size="30"
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221 value="unknown"
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222 label="UCSC Genome Browser assembly ID"
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223 />
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224 <param
0
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225 format="fasta"
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226 name="fasta_file"
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227 type="data"
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228 label="Reference genome"
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229 />
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230 <repeat name="group" title="New group">
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231 <param type="text" name="group_name" label="Group name" value="Default group"/>
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232 <repeat name="format" title="New track">
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233 <conditional name="formatChoice">
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234 <param name="format_select" type="select" label="Format">
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235 <option value="bam" selected="true">BAM</option>
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236 <option value="bed">BED</option>
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237 <option value="psl">PSL</option>
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238 <option value="bigwig">BIGWIG</option>
24
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239 <option value="bigbed">BIGBED</option>
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240 <option value="gff3">GFF3</option>
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241 <option value="gtf">GTF</option>
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242 </param>
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243
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244 <when value="bam">
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245 <param
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246 format="bam"
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247 name="BAM"
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248 type="data"
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249 label="BAM File"
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250 />
26
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251 <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" />
17
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252 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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253 <param name="track_color" type="color" label="Track color" value="#000000">
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254 <sanitizer>
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255 <valid initial="string.letters,string.digits">
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256 <add value="#"/>
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257 </valid>
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258 </sanitizer>
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259 </param>
24
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260 </when>
17
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261 <when value="bed">
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262 <conditional name="bedChoice">
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263 <param name="bed_select" type="select" label="Bed Choice">
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264 <option value="bed_generic" selected="true">BED Generic (bed4)</option>
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265 <option value="bed_cytoBand">cytoBand Track (bed4+1)</option>
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266 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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267 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
22
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268 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
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269 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
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270 </param>
20
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271 <when value="bed_generic">
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272 <param
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273 format="bed"
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274 name="BED"
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275 type="data"
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276 label="Generic Bed File Choice"
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277 />
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278
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279 </when>
24
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280 <when value="bed_cytoBand">
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281 <param
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282 format="bed"
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283 name="BED_cytoBand"
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284 type="data"
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285 label="cytoBand Track (Bed4)"
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286 />
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287 </when>
17
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288 <when value="bed_simple_repeats_option">
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289 <param
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290 format="bed"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
291 name="BED_simple_repeats"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
292 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
293 label="Bed Simple Repeats (Bed4+12) File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
294 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
295 </when>
20
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yating-l
parents: 18
diff changeset
296 <when value="bed_splice_junctions_option">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
297 <param
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
298 format="bed"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
299 name="BED_splice_junctions"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
300 type="data"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
301 label="Bed Splice Junctions (Bed12+1) File"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
302 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
303 </when>
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
304 <when value="bed_blast_alignment_option">
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
305 <param
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
306 format="bed"
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
307 name="BED_blast_alignment"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
308 type="data"
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
309 label="Bed Blast Alignments (Bed12+12) File"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
310 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
311 <param name="database" type="select" label="Protein database">
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
312 <option value="NCBI" selected="true">NCBI</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
313 <option value="UniProt">UniProt</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
314 <option value="FlyBase">FlyBase</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
315 <option value="Others">Others</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
316 </param>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
317 <expand macro="add_trix_file"/>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
318 </when>
22
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
319 <when value="bed_blat_alignment_option">
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
320 <param
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
321 format="bed"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
322 name="BED_blat_alignment"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
323 type="data"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
324 label="Bed BLAT Alignments (bigPsl) File"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
325 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
326 <param name="database" type="select" label="mRNA database">
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
327 <option value="NCBI" selected="true">NCBI</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
328 <option value="Others">Others</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
329 </param>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
330 <expand macro="add_trix_file"/>
22
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
331 </when>
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
332 </conditional>
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
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diff changeset
333 <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" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
334 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
335 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
336 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
337 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
338 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
339 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
340 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
341 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
342 <when value="psl">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
343 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
344 format="psl"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
345 name="PSL"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
346 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
347 label="PSL File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
348 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
349 <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" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
350 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
351 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
352 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
353 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
354 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
355 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
356 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
357 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
358 <when value="bigwig">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
359 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
360 format="bigwig"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
361 name="BIGWIG"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
362 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
363 label="BIGWIG File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
364 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
365 <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" />
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
366 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
367 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
368 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
369 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
370 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
371 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
372 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
373 </when>
24
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
374 <when value="bigbed">
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
375 <param
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
376 format="bigbed"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
377 name="BIGBED"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
378 type="data"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
379 label="BIGBED File"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
380 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
381 <expand macro="add_trix_file">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
382 <param
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
383 name="trix_id"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
384 value="name"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
385 type="text"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
386 size="30"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
387 label="Specify Trix identifier (The default is name)"
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388 />
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389 </expand>
26
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390 <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" />
24
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391 <param name="track_color" type="color" label="Track color" value="#000000">
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392 <sanitizer>
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393 <valid initial="string.letters,string.digits">
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394 <add value="#"/>
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395 </valid>
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396 </sanitizer>
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397 </param>
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398 </when>
17
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diff changeset
399 <when value="gff3">
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diff changeset
400 <param
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401 format="gff3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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402 name="GFF3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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403 type="data"
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404 label="GFF3 File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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405 />
26
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406 <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" />
17
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407 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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408 <sanitizer>
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409 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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410 <add value="#"/>
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411 </valid>
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412 </sanitizer>
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413 </param>
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414 </when>
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415 <when value="gtf">
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416 <param
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417 format="gtf"
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418 name="GTF"
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diff changeset
419 type="data"
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420 label="GTF File"
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421 />
26
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422 <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" />
17
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423 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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424 <sanitizer>
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diff changeset
425 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
426 <add value="#"/>
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427 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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428 </sanitizer>
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diff changeset
429 </param>
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430 </when>
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431 </conditional>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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432 </repeat>
0
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433 </repeat>
13
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diff changeset
434 <conditional name="advanced_options">
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435 <param name="advanced_options_selector" type="select" label="Advanced options">
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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436 <option value="off" selected="true">Hide advanced options</option>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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437 <option value="on">Display advanced options</option>
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438 </param>
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439 <!-- TODO: Avoid redundancy here -->
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440 <when value="on">
29
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441 <param name="debug_mode" type="select" label="Activate debug mode">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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442 <option value="false" selected="true">No</option>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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443 <option value="true">Yes</option>
13
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444 <help>
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445 Use this option if you are a G-OnRamp developer
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446 </help>
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447 </param>
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448 </when>
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449 <when value="off">
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450 <param name="debug_mode" type="hidden"
29
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451 value="false">
13
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452 </param>
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453 </when>
29
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454 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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455 </inputs>
0
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456
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457 <outputs>
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458 <data format="trackhub" name="output"/>
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459 </outputs>
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460
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461 <tests>
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462
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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463 <!-- Test with only the fasta file -->
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464 <test>
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465 <param name="genome_name" value="Dbia3"/>
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466 <param name="fasta_file" value="common/dbia3.fa"/>
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467 <output name="output" file="only_genome/only_genome.html">
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468 <!-- Use macro to check the whole common structure without repeated code -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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469 <expand macro="verify_hub_structure_no_track" test="only_genome" />
20
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470 </output>
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471 </test>
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472
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473 <!-- Test with Bam -->
0
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474 <test>
20
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475 <param name="genome_name" value="Dbia3"/>
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476 <param name="fasta_file" value="common/dbia3.fa"/>
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diff changeset
477 <repeat name="group">
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478 <param name="group_name" value="Default group"/>
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479 <repeat name="format">
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diff changeset
480 <conditional name="formatChoice">
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481 <param name="format_select" value="bam"/>
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482 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
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diff changeset
483 <param name="longLabel" value="HISAT sequence alignment" />
20
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diff changeset
484 <param name="track_color" value="#000000"/>
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diff changeset
485 </conditional>
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diff changeset
486 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
487 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
488 <output name="output" file="bam/bam.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
489 <!-- Verify tracks folder contains bam and bai -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
490 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
491 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
492 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
493 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
494 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
495 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
496 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
497 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
498 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
499 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
500 <!-- Use macro to check the whole common structure without repeated code -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
501 <expand macro="verify_hub_structure" test="bam" />
20
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yating-l
parents: 18
diff changeset
502 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
503 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
504
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
505 <!-- Test with Bed Generic -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
506 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
507 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
508 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
509 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
510 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
511 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
512 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
513 <param name="format_select" value="bed" />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
514 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
515 <param name="bed_select" value="bed_generic"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
516 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
517 <param name="longLabel" value="TBLASTN alignment" />
20
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yating-l
parents: 18
diff changeset
518 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
519 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
520 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
521 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
522 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
523 <output name="output" file="bed_generic/bed_generic.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
524 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
525 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
526 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
527 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
528 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
529 <expand macro="verify_hub_structure" test="bed_generic" />
20
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yating-l
parents: 18
diff changeset
530 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
531 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
532
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
533 <!-- Test with Bed Simple repeat -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
534 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
535 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
536 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
537 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
538 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
539 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
540 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
541 <param name="format_select" value="bed" />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
542 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
543 <param name="bed_select" value="bed_simple_repeats_option"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
544 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
545 <param name="longLabel" value="Simple repeat" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
546 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
547 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
548 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
549 </repeat>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
550 </repeat>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
551 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
552 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
553 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
554 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
555 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
556 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
557 <expand macro="verify_hub_structure" test="bed_simple_repeats" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
558 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
559 </test>
24
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
560
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
561 <!-- Test with Psl -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
562 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
563 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
564 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
565 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
566 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
567 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
568 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
569 <param name="format_select" value="psl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
570 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
571 <param name="longLabel" value="BLAST Alignment" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
572 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
573 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
574 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
575 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
576 <output name="output" file="psl/psl_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
577 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
578 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
579 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
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yating-l
parents: 18
diff changeset
580 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
581 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
582 <expand macro="verify_hub_structure" test="psl" />
20
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yating-l
parents: 18
diff changeset
583 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
584 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
585
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
586 <!-- Test with BigWig -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
587 <test>
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yating-l
parents: 18
diff changeset
588 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
589 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
590 <repeat name="group">
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yating-l
parents: 18
diff changeset
591 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
592 <repeat name="format">
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yating-l
parents: 18
diff changeset
593 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
594 <param name="format_select" value="bigwig"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
595 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
596 <param name="longLabel" value="RNA-Seq Coverage" />
20
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yating-l
parents: 18
diff changeset
597 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
598 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
599 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
600 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
601 <output name="output" file="bigwig/bigwig.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
602 <extra_files type="file"
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
603 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
604 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
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yating-l
parents: 18
diff changeset
605 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
606 />
29
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parents: 28
diff changeset
607 <expand macro="verify_hub_structure" test="bigwig" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
608 <!-- check additional trackDb settings for BigWig -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
609 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
610 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
611 <has_text text="autoScale"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
612 <has_text text="maxHeightPixels"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
613 <has_text text="windowingFunction"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
614 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
615 </extra_files>
20
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parents: 18
diff changeset
616 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
617 </test>
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yating-l
parents: 18
diff changeset
618
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
619 <!-- Test with GFF3 -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
620 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
621 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
622 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
623 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
624 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
625 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
626 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
627 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
628 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
629 <param name="longLabel" value="Augustus" />
20
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yating-l
parents: 18
diff changeset
630 <param name="track_color" value="#000000"/>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
631 </conditional>
20
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yating-l
parents: 18
diff changeset
632 </repeat>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
633 </repeat>
20
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yating-l
parents: 18
diff changeset
634 <output name="output" file="gff3/gff3_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
635 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
636 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
637 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
638 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
639 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
640 <expand macro="verify_hub_structure" test="gff3" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
641 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
642 </test>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
643
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
644 <!-- Test with GTF -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
645 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
646 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
647 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
648 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
649 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
650 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
651 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
652 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
653 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
654 <param name="longLabel" value="StringTie transcripts" />
20
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yating-l
parents: 18
diff changeset
655 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
656 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
657 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
658 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
659 <output name="output" file="gtf/gtf_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
660 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
661 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
662 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
663 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
664 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
665 <expand macro="verify_hub_structure" test="gtf" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
666 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
667 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
668
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
669 <!-- Test with BLAT Alignment -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
670 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
671 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
672 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
673 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
674 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
675 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
676 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
677 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
678 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
679 <param name="bed_select" value="bed_blat_alignment_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
680 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
681 <param name="longLabel" value="BLAT alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
682 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
683 <param name="database" value="NCBI" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
684 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
685 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
686 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
687 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
688 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
689 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
690 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
691 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
692 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
693 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
694 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
695 <!-- check additional trackDb settings for BLAT -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
696 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
697 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
698 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
699 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
700 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
701 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
702 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
703 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
704 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
705 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
706 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
707
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
708 <!-- Test with BLAST Alignment -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
709 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
710 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
711 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
712 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
713 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
714 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
715 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
716 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
717 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
718 <param name="bed_select" value="bed_blast_alignment_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
719 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
720 <param name="longLabel" value="BLAST alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
721 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
722 <param name="database" value="NCBI" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
723 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
724 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
725 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
726 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
727 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
728 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
729 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
730 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
731 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
732 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
733 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
734 <!-- check additional trackDb settings for BLAST -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
735 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
736 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
737 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
738 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
739 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
740 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
741 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
742 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
743 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
744 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
745 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
746
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
747 <!-- Test with Regtools Splice Junctions -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
748 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
749 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
750 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
751 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
752 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
753 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
754 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
755 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
756 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
757 <param name="bed_select" value="bed_splice_junctions_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
758 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
759 <param name="longLabel" value="Splice junctions" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
760 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
761 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
762 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
763 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
764 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
765 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
766 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
767 name="myHub/Dbia3/tracks/regtools_junctions.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
768 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
769 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
770 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
771 <expand macro="verify_hub_structure" test="bed_splice_junctions" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
772 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
773 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
774
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
775 <!-- Test with Cytoband -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
776 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
777 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
778 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
779 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
780 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
781 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
782 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
783 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
784 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
785 <param name="bed_select" value="bed_cytoBand"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
786 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
787 <param name="longLabel" value="Cytoband" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
788 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
789 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
790 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
791 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
792 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
793 <output name="output" file="bed_cytoband/cytoband_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
794 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
795 name="myHub/Dbia3/tracks/Cytoband.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
796 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
797 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
798 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
799 <expand macro="verify_hub_structure" test="bed_cytoband" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
800 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
801 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
802 <has_text text="track cytoBandIdeo"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
803 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
804 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
805 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
806 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
807
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
808 <!-- Test with bigBed -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
809 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
810 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
811 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
812 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
813 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
814 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
815 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
816 <param name="format_select" value="bigbed"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
817 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
818 <param name="longLabel" value="bigBed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
819 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
820 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
821 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
822 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
823 <output name="output" file="big_bed/bigbed_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
824 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
825 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
826 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
827 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
828 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
829 <expand macro="verify_hub_structure" test="big_bed" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
830 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
831 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
832
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
833 <!-- Test with one group and multiple tracks -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
834 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
835 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
836 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
837 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
838 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
839 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
840 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
841 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
842 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
843 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
844 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
845 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
846 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
847 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
848 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
849 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
850 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
851 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
852 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
853 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
854 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
855 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
856 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
857 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
858 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
859 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
860 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
861 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
862 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
863 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
864 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
865 <expand macro="verify_hub_structure" test="gtf_gff" />
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
866 </output>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
867 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
868
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
869 <!-- Test with one group and all the supported datatypes -->
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
870 <test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
871 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
872 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
873 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
874 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
875 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
876 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
877 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
878 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
879 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
880 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
881 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
882 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
883 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
884 <param name="format_select" value="bed"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
885 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
886 <param name="bed_select" value="bed_generic"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
887 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
888 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
889 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
890 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
891 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
892 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
893 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
894 <param name="format_select" value="bed"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
895 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
896 <param name="bed_select" value="bed_simple_repeats_option"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
897 <param name="BED_simple_repeats" ftype="bed"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
898 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
899 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
900 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
901 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
902 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
903 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
904 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
905 <param name="format_select" value="psl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
906 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
907 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
908 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
909 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
910 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
911 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
912 <param name="format_select" value="bigwig"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
913 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
914 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
915 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
916 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
917 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
918 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
919 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
920 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
921 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
922 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
923 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
924 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
925 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
926 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
927 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
928 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
929 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
930 </repeat>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
931 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
932 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
933 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
934 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
935 <param name="bed_select" value="bed_cytoBand"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
936 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
937 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
938 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
939 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
940 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
941 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
942 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
943 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
944 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
945 <param name="bed_select" value="bed_splice_junctions_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
946 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
947 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
948 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
949 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
950 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
951 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
952 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
953 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
954 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
955 <param name="bed_select" value="bed_blast_alignment_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
956 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
957 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
958 <param name="database" value="NCBI" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
959 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
960 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
961 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
962 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
963 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
964 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
965 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
966 <param name="bed_select" value="bed_blat_alignment_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
967 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
968 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
969 <param name="database" value="NCBI" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
970 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
971 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
972 </repeat>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
973 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
974 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
975 <!-- verify tracks folder contains all the files -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
976 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
977 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
978 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
979 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
980 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
981 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
982 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
983 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
984 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
985 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
986 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
987 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
988 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
989 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
990 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
991 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
992 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
993 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
994 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
995 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
996 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
997 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
998 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
999 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1000 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1001 <extra_files type="file"
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1002 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1003 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1004 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1005 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1006 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1007 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1008 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1009 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1010 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1011 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1012 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1013 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1014 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1015 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1016 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1017 name="myHub/Dbia3/tracks/Cytoband.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1018 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1019 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1020 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1021 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1022 name="myHub/Dbia3/tracks/regtools_junctions.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1023 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1024 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1025 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1026 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1027 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1028 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1029 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1030 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1031 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1032 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1033 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1034 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1035 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1036 <expand macro="verify_hub_structure" test="all_datatypes" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1037 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1038 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1039
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1040 <!-- Test with two groups and no tracks -->
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1041 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1042 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1043 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1044 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1045 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1046 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1047 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1048 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1049 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1050 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1051 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1052 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1053 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1054
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1055 <!-- Test with two groups and one track in first -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1056 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1057 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1058 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1059 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1060 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1061 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1062 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1063 <param name="format_select" value="bigwig"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1064 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
20
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yating-l
parents: 18
diff changeset
1065 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1066 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1067 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1068 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1069 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1070 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1071 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1072 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1073 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1074 <extra_files type="file"
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1075 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1076 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1077 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1078 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1079 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1080 </output>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1081 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1082
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1083 <!-- Test with two groups and one track in both -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1084 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1085 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1086 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1087 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1088 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1089 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1090 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1091 <param name="format_select" value="bigwig"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
1092 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
20
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yating-l
parents: 18
diff changeset
1093 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1094 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1095 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1096 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1097 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1098 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1099 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1100 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1101 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1102 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1103 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1104 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1105 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1106 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1107 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1108 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1109 <!-- First group -->
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yating-l
parents: 18
diff changeset
1110 <extra_files type="file"
29
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parents: 28
diff changeset
1111 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1112 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
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parents: 18
diff changeset
1113 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1114 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1115
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1116 <!-- Second group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1117 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1118 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1119 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1120 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1121 />
29
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yating-l
parents: 28
diff changeset
1122 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
20
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yating-l
parents: 18
diff changeset
1123 <!-- Check the groups.txt exists and is properly populated -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1124 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1125 </test>
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parents: 18
diff changeset
1126
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parents: 18
diff changeset
1127 <!-- Test with two groups and multiple tracks in both -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1128 <test>
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yating-l
parents: 18
diff changeset
1129 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1130 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1131 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1132 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1133 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1134 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1135 <param name="format_select" value="bigwig"/>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
1136 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1137 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1138 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1139 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1140 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1141 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1142 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1143 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1144 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1145 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1146 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1147 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1148 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1149 <param name="group_name" value="Other group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1150 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1151 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1152 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1153 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1154 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1155 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1156 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1157 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1158 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1159 <param name="format_select" value="gff3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1160 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1161 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1162 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1163 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1164 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1165 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1166 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1167 <!-- First group -->
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yating-l
parents: 18
diff changeset
1168 <extra_files type="file"
29
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parents: 28
diff changeset
1169 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1170 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1171 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1172 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1173 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1174 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1175 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1176 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1177 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1178 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1179 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1180 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1181 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1182 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1183
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1184 <!-- Second group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1185 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1186 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1187 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1188 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1189 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1190 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1191 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1192 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1193 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1194 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1195 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1196 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1197 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1198
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1199 <!-- Test default color in a track -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1200 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1201 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1202 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1203 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1204 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1205 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1206 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1207 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1208 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1209 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1210 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1211 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1212 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1213 <output name="output" file="default_color/default_color_trackhub.html">
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1214 <expand macro="verify_hub_structure" test="default_color" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1215 <!-- Verify trackDb.txt contains the color 0,0,0 -->
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1216 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
20
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yating-l
parents: 18
diff changeset
1217 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1218 <has_text text="color 0,0,0"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1219 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1220 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1221
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1222 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1223 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1224 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1225
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1226 <!-- Test changed color in a track -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1227 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1228 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1229 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1230 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1231 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1232 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1233 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1234 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1235 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1236 <param name="track_color" value="#8064a2"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1237 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1238 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1239 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1240 <output name="output" file="changed_color/changed_color_trackhub.html">
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1241 <expand macro="verify_hub_structure" test="changed_color" />
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1242 <!-- Verify trackDb.txt contains the color 128,100,162 -->
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1243 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1244 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1245 <has_text text="color 128,100,162"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1246 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1247 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1248
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1249 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1250 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1251 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1252
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1253 <!-- Test for StringTie Chromosome end coordinates -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1254 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1255 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1256 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1257 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1258 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1259 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1260 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1261 <param name="format_select" value="gtf"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1262 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1263 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1264 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1265 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1266 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1267 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1268 <extra_files type="file"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1269 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1270 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1271 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1272 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1273 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1274
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1275 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1276 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1277 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1278
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1279 <!-- Test default label in a track -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1280 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1281 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1282 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1283 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1284 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1285 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1286 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1287 <param name="format_select" value="bam"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1288 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1289 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1290 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1291 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1292 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1293 <output name="output" file="default_color/default_color_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1294 <expand macro="verify_hub_structure" test="default_color" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1295 <!-- Verify trackDb.txt contains default label -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1296 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1297 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1298 <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1299 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1300 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1301
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1302 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1303 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1304 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1305
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1306 <!-- Test customized label in a track -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1307 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1308 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1309 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1310 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1311 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1312 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1313 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1314 <param name="format_select" value="bam"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1315 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1316 <param name="longLabel" value="HISAT sequence alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1317 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1318 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1319 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1320 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1321 <output name="output" file="changed_label/changed_label_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1322 <expand macro="verify_hub_structure" test="changed_label" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1323 <!-- Verify trackDb.txt contains the customized label -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1324 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1325 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1326 <has_text text="longLabel HISAT sequence alignment"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1327 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1328 </extra_files>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1329
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1330 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1331 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1332 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1333
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1334 <!-- Test TrixIndex for Blat alignment track -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1335 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1336 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1337 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1338 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1339 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1340 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1341 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1342 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1343 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1344 <param name="bed_select" value="bed_blat_alignment_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1345 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1346 <param name="longLabel" value="BLAT alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1347 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1348 <param name="database" value="NCBI" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1349 <conditional name="add_trix_index">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1350 <param name="add_trix_index_selector" value="yes" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1351 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1352 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1353 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1354 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1355 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1356 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1357 <param name="debug_mode" value="true" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1358 <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1359 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1360 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1361 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1362 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1363 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1364 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1365 <!-- check additional trackDb settings for BLAT -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1366 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1367 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1368 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1369 <has_text text="searchTrix"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1370 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1371 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1372 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1373 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1374 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1375 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1376 <!-- check Trix index directory -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1377 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1378 value="trix_index_files/blat_out.ix" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1379 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1380 value="trix_index_files/blat_out.ixx" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1381 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1382 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1383
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1384 <!-- Test TrixIndex for BLAST Alignment -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1385 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1386 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1387 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1388 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1389 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1390 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1391 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1392 <param name="format_select" value="bed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1393 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1394 <param name="bed_select" value="bed_blast_alignment_option"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1395 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1396 <param name="longLabel" value="BLAST alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1397 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1398 <param name="database" value="NCBI" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1399 <conditional name="add_trix_index">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1400 <param name="add_trix_index_selector" value="yes" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1401 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1402 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1403 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1404 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1405 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1406 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1407 <param name="debug_mode" value="true" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1408 <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1409 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1410 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1411 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1412 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1413 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1414 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1415 <!-- check additional trackDb settings for BLAST -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1416 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1417 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1418 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1419 <has_text text="searchTrix"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1420 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1421 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1422 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1423 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1424 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1425 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1426 <!-- check Trix index directory -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1427 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1428 value="trix_index_files/blast_out.ix" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1429 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1430 value="trix_index_files/blast_out.ixx" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1431 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1432 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1433
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1434 <!-- Test TrixIndex for BigBed -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1435 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1436 <param name="genome_name" value="Dbia3"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1437 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1438 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1439 <param name="group_name" value="Default group"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1440 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1441 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1442 <param name="format_select" value="bigbed"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1443 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1444 <param name="longLabel" value="bigBed" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1445 <param name="track_color" value="#000000"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1446 <conditional name="add_trix_index">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1447 <param name="add_trix_index_selector" value="yes" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1448 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1449 <param name="trix_id" value="name" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1450 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1451 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1452 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1453 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1454 <param name="debug_mode" value="true" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1455 <output name="output" file="trix_index_files/bigbed_trackhub.html">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1456 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1457 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1458 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1459 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1460 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1461 <expand macro="verify_hub_structure" test="big_bed">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1462 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1463 <has_text text="searchTrix"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1464 </expand>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1465
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1466 <!-- check Trix index directory -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1467 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1468 value="trix_index_files/blat_out.ix" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1469 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1470 value="trix_index_files/blat_out.ixx" />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1471 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1472 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1473
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1474 </tests>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1475
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1476 <help>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1477 This Galaxy tool permits to prepare your files to be ready for
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1478 Assembly Hub visualization.
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1479 </help>
24
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1480
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1481 <citations>
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1482 <citation type="doi">10.7490/f1000research.1112719.1</citation>
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1483 </citations>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1484 </tool>