Mercurial > repos > rmarenco > hubarchivecreator

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5a0c39ed61b4408ba65a759aede807df260d097d
author yating-l
date Sun, 26 Aug 2018 16:44:27 -0400
parents 9c5d82d3c87e
children
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.3">
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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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38 <environment_variables>
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39 <!-- Sort uppercase letters before lowercase (required by UCSC tools) -->
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40 <environment_variable name="LC_COLLATE">C</environment_variable>
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41 </environment_variables>
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43 <configfiles>
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44 <configfile name="json_file">
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45 import json
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46 import sys
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48 file_path = sys.argv[1]
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49 #set global $data_parameter_dict = {}
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51 ## Ask the user to enter the genome name
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52 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
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54 ## Function to retrieve the data of the inputs
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55 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
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56 #set false_path = str($input_to_prepare)
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57 #set $data_dict = {"false_path": $false_path}
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59 #set name = str($input_to_prepare.name)
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60 #silent $data_dict.update({"name": $name})
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61 #silent $data_dict.update($extra_data_dict)
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62 ## Add the ordering by taking the tool form indexes
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63 #silent $data_dict.update({"order_index": $order_index})
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65 #if $datatype in $data_parameter_dict
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66 #silent $data_parameter_dict[$datatype].append($data_dict)
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67 #else
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68 #set array_inputs = []
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69 #silent $array_inputs.append($data_dict)
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70 #silent $data_parameter_dict.update({$datatype: $array_inputs})
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71 #end if
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72 #end def
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74 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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76 #set temp_max_digit = 0
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78 #for $g in $group
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79 #if len($g.format) > $temp_max_digit
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80 #silent temp_max_digit = len($g.format)
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81 #end if
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82 #end for
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85 #set nb_digits_max_track = len(str($temp_max_digit))
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87 ## END Get the number of digits
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89 #for $i_g, $g in enumerate( $group )
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90 #for $i, $f in enumerate( $g.format )
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91 ## Create the order index using index_group+1 concatenated with index_track
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92 #set index_group_final = str($i_g + 1)
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93 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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95 ## For each format, we have a few mandatory fields we store in a dict
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96 #set track_color = str($f.formatChoice.track_color)
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97 #set group_name = str($g.group_name)
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98 #set longLabel = str($f.formatChoice.longLabel)
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99 #set extra_data_dict = {"track_color": $track_color,
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100 "group_name": $group_name,
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101 "long_label": $longLabel}
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103 #if $f.formatChoice.format_select == "bam"
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104 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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105
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106 ## Add Bam format specific fields
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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107 #silent $extra_data_dict.update({"index": $bam_index})
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
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108
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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109 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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110 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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111 #if $f.formatChoice.format_select == "bed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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112 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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113 #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
yating-l
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114 $extra_data_dict)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
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115 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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116 #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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117 #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
yating-l
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118 $extra_data_dict)
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yating-l
parents: 28
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119 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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120 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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121 #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
yating-l
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122 $extra_data_dict)
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yating-l
parents: 28
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123 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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124 #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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125 #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
yating-l
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126 $extra_data_dict)
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yating-l
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127 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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128 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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129 #set database = str($f.formatChoice.bedChoice.database)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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130 #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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131 #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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132 #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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133 #if $i.element_identifier.endswith("ix")
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134 #$extra_data_dict.update({"index_ix": str($i)})
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135 #elif $i.element_identifier.endswith("ixx")
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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136 #$extra_data_dict.update({"index_ixx": str($i)})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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137 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
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138 #end for
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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139 ##set ix_index = str($f.formatChoice.bedChoice.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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140 ##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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141 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
0
0f3bc17e5ede Uploaded
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142 #end if
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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143 #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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144 $extra_data_dict)
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145 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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146 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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147 #set database = str($f.formatChoice.bedChoice.database)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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148 #silent $extra_data_dict.update({"database": $database})
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149 #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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150 #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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151 #if $i.element_identifier.endswith("ix")
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152 #$extra_data_dict.update({"index_ix": str($i)})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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153 #elif $i.element_identifier.endswith("ixx")
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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154 #$extra_data_dict.update({"index_ixx": str($i)})
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155 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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156 #end for
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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157 ##set ix_index = str($f.formatChoice.bedChoice.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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158 ##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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159 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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160 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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161 #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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162 $extra_data_dict)
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163 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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164 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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165 #if $f.formatChoice.format_select == "psl"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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166 #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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167 $extra_data_dict)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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168 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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169 #if $f.formatChoice.format_select == "bigwig"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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170 #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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171 $extra_data_dict)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
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172 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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173 #if $f.formatChoice.format_select == "bigbed"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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174 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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175 ##set ix_index = str($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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176 ##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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177 #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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178 #if $i.element_identifier.endswith("ix")
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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179 #$extra_data_dict.update({"index_ix": str($i)})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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180 #elif $i.element_identifier.endswith("ixx")
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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181 #$extra_data_dict.update({"index_ixx": str($i)})
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40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
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182 #end if
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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183 #end for
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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184 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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185 ##set trix_id = str($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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186 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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187 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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188 #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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189 $extra_data_dict)
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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190 #end if
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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191 #if $f.formatChoice.format_select == "gff3"
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192 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
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193 $extra_data_dict)
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194 #end if
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195 #if $f.formatChoice.format_select == "gtf"
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196 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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197 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
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198 $extra_data_dict)
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199 #end if
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200 #end for
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201 #end for
0
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202
29
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203 ## We combine the fasta file dataset name with his false path in a JSON object
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204 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
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205 $data_parameter_dict.update({"fasta": $fasta_json})
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206
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207 ## Retrieve the user email
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208 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
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209
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210 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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211
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212 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
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213
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214 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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215
29
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216 with open(file_path, 'w') as f:
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217 json.dump($data_parameter_dict, f)
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218
29
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219 </configfile>
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220 </configfiles>
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221
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222 <inputs>
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223 <param
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224 name="genome_name"
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225 type="text"
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226 size="30"
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227 value="unknown"
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228 label="UCSC Genome Browser assembly ID"
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229 />
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230 <param
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231 format="fasta"
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232 name="fasta_file"
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233 type="data"
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234 label="Reference genome"
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235 />
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236 <repeat name="group" title="New group">
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237 <param type="text" name="group_name" label="Group name" value="Default group"/>
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238 <repeat name="format" title="New track">
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239 <conditional name="formatChoice">
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240 <param name="format_select" type="select" label="Format">
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241 <option value="bam" selected="true">BAM</option>
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242 <option value="bed">BED</option>
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243 <option value="psl">PSL</option>
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244 <option value="bigwig">BIGWIG</option>
24
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245 <option value="bigbed">BIGBED</option>
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246 <option value="gff3">GFF3</option>
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247 <option value="gtf">GTF</option>
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248 </param>
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249
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250 <when value="bam">
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251 <param
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252 format="bam"
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253 name="BAM"
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254 type="data"
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255 label="BAM File"
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256 />
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257 <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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258 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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259 <param name="track_color" type="color" label="Track color" value="#000000">
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260 <sanitizer>
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261 <valid initial="string.letters,string.digits">
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262 <add value="#"/>
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263 </valid>
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264 </sanitizer>
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265 </param>
24
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266 </when>
17
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267 <when value="bed">
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268 <conditional name="bedChoice">
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269 <param name="bed_select" type="select" label="Bed Choice">
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270 <option value="bed_generic" selected="true">BED Generic</option>
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271 <option value="bed_cytoBand">cytoBand Track (bed4+1)</option>
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272 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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273 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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274 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
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275 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
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276 </param>
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277 <when value="bed_generic">
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278 <param
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279 format="bed"
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280 name="BED"
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281 type="data"
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282 label="Generic Bed File Choice"
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283 />
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284
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285 </when>
24
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286 <when value="bed_cytoBand">
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287 <param
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288 format="bed"
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289 name="BED_cytoBand"
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diff changeset
290 type="data"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
291 label="cytoBand Track (Bed4)"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
292 />
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
293 </when>
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
294 <when value="bed_simple_repeats_option">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
295 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
296 format="bed"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
297 name="BED_simple_repeats"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
298 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
299 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
300 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
301 </when>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
302 <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
303 <param
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
304 format="bed"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
305 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
306 type="data"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
307 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
308 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
309 </when>
21
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yating-l
parents: 20
diff changeset
310 <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
311 <param
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
312 format="bed"
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
313 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
314 type="data"
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 20
diff changeset
315 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
316 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
317 <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
318 <option value="NCBI" selected="true">NCBI</option>
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
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diff changeset
319 <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
320 <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
321 <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
322 </param>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
323 <expand macro="add_trix_file"/>
20
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yating-l
parents: 18
diff changeset
324 </when>
22
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
325 <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
326 <param
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
327 format="bed"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
328 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
329 type="data"
7ddf651457df planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 21
diff changeset
330 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
331 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
332 <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
333 <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
334 <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
335 </param>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
336 <expand macro="add_trix_file"/>
22
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yating-l
parents: 21
diff changeset
337 </when>
17
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
338 </conditional>
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
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diff changeset
339 <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
340 <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
341 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
342 <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
343 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
344 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
345 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
346 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
347 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
348 <when value="psl">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
349 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
350 format="psl"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
351 name="PSL"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
352 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
353 label="PSL File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
354 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
355 <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
356 <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
357 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
358 <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
359 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
360 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
361 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
362 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
363 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
364 <when value="bigwig">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
365 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
366 format="bigwig"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
367 name="BIGWIG"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
368 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
369 label="BIGWIG File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
370 />
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 24
diff changeset
371 <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
372 <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
373 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
374 <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
375 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
376 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
377 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
378 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents: 16
diff changeset
379 </when>
24
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
380 <when value="bigbed">
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
381 <param
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
382 format="bigbed"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
383 name="BIGBED"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
384 type="data"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
385 label="BIGBED File"
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
386 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
387 <expand macro="add_trix_file">
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diff changeset
388 <param
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diff changeset
389 name="trix_id"
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diff changeset
390 value="name"
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diff changeset
391 type="text"
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diff changeset
392 size="30"
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diff changeset
393 label="Specify Trix identifier (The default is name)"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
394 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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diff changeset
395 </expand>
26
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diff changeset
396 <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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diff changeset
397 <param name="track_color" type="color" label="Track color" value="#000000">
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diff changeset
398 <sanitizer>
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diff changeset
399 <valid initial="string.letters,string.digits">
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parents: 23
diff changeset
400 <add value="#"/>
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401 </valid>
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parents: 23
diff changeset
402 </sanitizer>
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parents: 23
diff changeset
403 </param>
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404 </when>
17
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diff changeset
405 <when value="gff3">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
406 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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407 format="gff3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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408 name="GFF3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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409 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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410 label="GFF3 File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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411 />
26
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412 <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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413 <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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414 <sanitizer>
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diff changeset
415 <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
416 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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417 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
418 </sanitizer>
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diff changeset
419 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
420 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
421 <when value="gtf">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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parents: 16
diff changeset
422 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
423 format="gtf"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
424 name="GTF"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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parents: 16
diff changeset
425 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
426 label="GTF File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
427 />
26
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428 <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
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diff changeset
429 <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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diff changeset
430 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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parents: 16
diff changeset
431 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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parents: 16
diff changeset
432 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
433 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
434 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
435 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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parents: 16
diff changeset
436 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
437 </conditional>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
438 </repeat>
0
0f3bc17e5ede Uploaded
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diff changeset
439 </repeat>
13
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diff changeset
440 <conditional name="advanced_options">
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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441 <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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442 <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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diff changeset
443 <option value="on">Display advanced options</option>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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parents: 11
diff changeset
444 </param>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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diff changeset
445 <!-- TODO: Avoid redundancy here -->
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446 <when value="on">
29
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diff changeset
447 <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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448 <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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diff changeset
449 <option value="true">Yes</option>
13
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parents: 11
diff changeset
450 <help>
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diff changeset
451 Use this option if you are a G-OnRamp developer
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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diff changeset
452 </help>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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453 </param>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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454 </when>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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455 <when value="off">
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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456 <param name="debug_mode" type="hidden"
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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457 value="false">
13
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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458 </param>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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459 </when>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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diff changeset
460 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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diff changeset
461 </inputs>
0
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462
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463 <outputs>
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464 <data format="trackhub" name="output"/>
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465 </outputs>
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466
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467 <tests>
29
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diff changeset
468
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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469 <!-- Test with only the fasta file -->
20
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470 <test>
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471 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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472 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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473 <output name="output" file="only_genome/only_genome.html">
29
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diff changeset
474 <!-- 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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diff changeset
475 <expand macro="verify_hub_structure_no_track" test="only_genome" />
20
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diff changeset
476 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
477 </test>
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parents: 18
diff changeset
478
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yating-l
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diff changeset
479 <!-- Test with Bam -->
0
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diff changeset
480 <test>
20
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parents: 18
diff changeset
481 <param name="genome_name" value="Dbia3"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
482 <param name="fasta_file" value="common/dbia3.fa"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
483 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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diff changeset
484 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
485 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
486 <conditional name="formatChoice">
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parents: 18
diff changeset
487 <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
488 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
29
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parents: 28
diff changeset
489 <param name="longLabel" value="HISAT sequence alignment" />
20
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parents: 18
diff changeset
490 <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
491 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
492 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
493 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
494 <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
495 <!-- 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
496 <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
497 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
498 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
499 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
500 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
501 <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
502 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
503 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
504 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
505 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
506 <!-- 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
507 <expand macro="verify_hub_structure" test="bam" />
20
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yating-l
parents: 18
diff changeset
508 </output>
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yating-l
parents: 18
diff changeset
509 </test>
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yating-l
parents: 18
diff changeset
510
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
511 <!-- 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
512 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
513 <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
514 <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
515 <repeat name="group">
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yating-l
parents: 18
diff changeset
516 <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
517 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
518 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
519 <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
520 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
521 <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
522 <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
523 <param name="longLabel" value="TBLASTN alignment" />
20
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yating-l
parents: 18
diff changeset
524 <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
525 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
526 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
527 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
528 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
529 <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
530 <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
531 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
532 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
533 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
534 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
535 <expand macro="verify_hub_structure" test="bed_generic" />
20
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yating-l
parents: 18
diff changeset
536 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
537 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
538
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
539 <!-- 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
540 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
541 <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
542 <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
543 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
544 <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
545 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
546 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
547 <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
548 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
549 <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
550 <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
551 <param name="longLabel" value="Simple repeat" />
20
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yating-l
parents: 18
diff changeset
552 <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
553 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
554 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
555 </repeat>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
556 </repeat>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
557 <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
558 <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
559 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
560 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
561 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
562 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
563 <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
564 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
565 </test>
24
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
566
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
567 <!-- Test with Psl -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
568 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
569 <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
570 <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
571 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
572 <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
573 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
574 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
575 <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
576 <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
577 <param name="longLabel" value="BLAST Alignment" />
20
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yating-l
parents: 18
diff changeset
578 <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
579 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
580 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
581 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
582 <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
583 <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
584 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
585 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
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yating-l
parents: 18
diff changeset
586 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
587 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
588 <expand macro="verify_hub_structure" test="psl" />
20
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yating-l
parents: 18
diff changeset
589 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
590 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
591
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
592 <!-- Test with BigWig -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
593 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
594 <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
595 <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
596 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
597 <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
598 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
599 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
600 <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
601 <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
602 <param name="longLabel" value="RNA-Seq Coverage" />
20
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yating-l
parents: 18
diff changeset
603 <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
604 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
605 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
606 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
607 <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
608 <extra_files type="file"
29
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parents: 28
diff changeset
609 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
610 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
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yating-l
parents: 18
diff changeset
611 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
612 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
613 <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
614 <!-- 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
615 <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
616 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
617 <has_text text="autoScale"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
618 <has_text text="maxHeightPixels"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
619 <has_text text="windowingFunction"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
620 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
621 </extra_files>
20
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parents: 18
diff changeset
622 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
623 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
624
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
625 <!-- Test with GFF3 -->
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yating-l
parents: 18
diff changeset
626 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
627 <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
628 <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
629 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
630 <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
631 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
632 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
633 <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
634 <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
635 <param name="longLabel" value="Augustus" />
20
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parents: 18
diff changeset
636 <param name="track_color" value="#000000"/>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
637 </conditional>
20
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yating-l
parents: 18
diff changeset
638 </repeat>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
639 </repeat>
20
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yating-l
parents: 18
diff changeset
640 <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
641 <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
642 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
643 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
644 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
645 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
646 <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
647 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
648 </test>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
649
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
650 <!-- Test with GTF -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
651 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
652 <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
653 <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
654 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
655 <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
656 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
657 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
658 <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
659 <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
660 <param name="longLabel" value="StringTie transcripts" />
20
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yating-l
parents: 18
diff changeset
661 <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
662 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
663 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
664 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
665 <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
666 <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
667 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
668 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
669 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
670 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
671 <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
672 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
673 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
674
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
675 <!-- Test with BLAT Alignment -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
676 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
677 <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
678 <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
679 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
680 <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
681 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
682 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
683 <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
684 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
685 <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
686 <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
687 <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
688 <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
689 <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
690 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
691 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
692 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
693 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
694 <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
695 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
696 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
697 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
698 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
699 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
700 <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
701 <!-- 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
702 <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
703 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
704 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
705 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
706 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
707 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
708 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
709 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
710 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
711 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
712 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
713
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
714 <!-- Test with BLAST Alignment -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
715 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
716 <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
717 <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
718 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
719 <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
720 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
721 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
722 <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
723 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
724 <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
725 <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
726 <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
727 <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
728 <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
729 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
730 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
731 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
732 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
733 <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
734 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
735 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
736 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
737 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
738 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
739 <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
740 <!-- 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
741 <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
742 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
743 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
744 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
745 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
746 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
747 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
748 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
749 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
750 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
751 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
752
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
753 <!-- 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
754 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
755 <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
756 <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
757 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
758 <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
759 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
760 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
761 <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
762 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
763 <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
764 <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
765 <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
766 <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
767 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
768 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
769 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
770 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
771 <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
772 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
773 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
774 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
775 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
776 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
777 <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
778 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
779 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
780
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
781 <!-- Test with Cytoband -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
782 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
783 <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
784 <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
785 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
786 <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
787 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
788 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
789 <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
790 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
791 <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
792 <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
793 <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
794 <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
795 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
796 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
797 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
798 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
799 <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
800 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
801 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
802 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
803 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
804 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
805 <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
806 <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
807 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
808 <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
809 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
810 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
811 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
812 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
813
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
814 <!-- Test with bigBed -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
815 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
816 <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
817 <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
818 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
819 <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
820 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
821 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
822 <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
823 <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
824 <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
825 <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
826 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
827 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
828 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
829 <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
830 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
831 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
832 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
833 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
834 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
835 <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
836 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
837 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
838
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
839 <!-- 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
840 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
841 <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
842 <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
843 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
844 <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
845 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
846 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
847 <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
848 <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
849 <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
850 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
851 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
852 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
853 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
854 <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
855 <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
856 <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
857 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
858 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
859 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
860 <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
861 <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
862 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
863 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
864 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
865 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
866 <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
867 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
868 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
869 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
870 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
871 <expand macro="verify_hub_structure" test="gtf_gff" />
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
872 </output>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
873 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
874
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
875 <!-- Test with one group and all the supported datatypes -->
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
876 <test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
877 <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
878 <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
879 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
880 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
881 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
882 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
883 <param name="format_select" value="bam"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
884 <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
885 <param name="track_color" value="#000000"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
886 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
887 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
888 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
889 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
890 <param name="format_select" value="bed"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
891 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
892 <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
893 <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
894 <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
895 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
896 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
897 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
898 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
899 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
900 <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
901 <conditional name="bedChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
902 <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
903 <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
904 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
905 <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
906 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
907 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
908 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
909 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
910 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
911 <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
912 <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
913 <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
914 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
915 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
916 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
917 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
918 <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
919 <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
920 <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
921 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
922 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
923 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
924 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
925 <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
926 <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
927 <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
928 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
929 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
930 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
931 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
932 <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
933 <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
934 <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
935 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
936 </repeat>
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
937 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
938 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
939 <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
940 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
941 <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
942 <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
943 <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
944 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
945 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
946 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
947 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
948 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
949 <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
950 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
951 <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
952 <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
953 <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
954 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
955 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
956 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
957 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
958 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
959 <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
960 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
961 <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
962 <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
963 <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
964 <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
965 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
966 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
967 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
968 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
969 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
970 <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
971 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
972 <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
973 <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
974 <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
975 <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
976 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
977 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
978 </repeat>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
979 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
980 <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
981 <!-- 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
982 <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
983 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
984 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
985 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
986 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
987 <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
988 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
989 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
990 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
991 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
992 <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
993 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
994 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
995 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
996 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
997 <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
998 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
999 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
1000 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1001 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1002 <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
1003 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
1004 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
1005 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1006 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1007 <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
1008 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
1009 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
1010 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1011 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1012 <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
1013 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
1014 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
1015 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1016 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1017 <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
1018 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
1019 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
1020 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1021 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1022 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1023 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
1024 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
1025 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1026 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1027 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1028 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
1029 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
1030 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1031 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1032 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1033 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
1034 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
1035 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1036 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1037 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1038 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
1039 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
1040 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1041 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1042 <expand macro="verify_hub_structure" test="all_datatypes" />
20
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yating-l
parents: 18
diff changeset
1043 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1044 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1045
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1046 <!-- 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
1047 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1048 <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
1049 <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
1050 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1051 <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
1052 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1053 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1054 <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
1055 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1056 <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
1057 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
20
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yating-l
parents: 18
diff changeset
1058 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1059 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1060
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1061 <!-- 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
1062 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1063 <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
1064 <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
1065 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1066 <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
1067 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1068 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1069 <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
1070 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
20
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yating-l
parents: 18
diff changeset
1071 <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
1072 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1073 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1074 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1075 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1076 <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
1077 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1078 <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
1079 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1080 <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
1081 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
1082 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
1083 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1084 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1085 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1086 </output>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1087 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1088
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1089 <!-- 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
1090 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1091 <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
1092 <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
1093 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1094 <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
1095 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1096 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1097 <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
1098 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
20
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yating-l
parents: 18
diff changeset
1099 <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
1100 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1101 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1102 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1103 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1104 <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
1105 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1106 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1107 <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
1108 <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
1109 <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
1110 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1111 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1112 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1113 <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
1114 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1115 <!-- First group -->
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yating-l
parents: 18
diff changeset
1116 <extra_files type="file"
29
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parents: 28
diff changeset
1117 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
1118 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
20
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parents: 18
diff changeset
1119 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
1120 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1121
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1122 <!-- Second group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1123 <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
1124 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
1125 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
1126 compare="sim_size"
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parents: 18
diff changeset
1127 />
29
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parents: 28
diff changeset
1128 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
20
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yating-l
parents: 18
diff changeset
1129 <!-- 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
1130 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1131 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1132
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yating-l
parents: 18
diff changeset
1133 <!-- Test with two groups and multiple tracks in both -->
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parents: 18
diff changeset
1134 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1135 <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
1136 <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
1137 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1138 <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
1139 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1140 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1141 <param name="format_select" value="bigwig"/>
29
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parents: 28
diff changeset
1142 <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
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parents: 18
diff changeset
1143 <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
1144 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1145 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1146 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1147 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1148 <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
1149 <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
1150 <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
1151 </conditional>
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yating-l
parents: 18
diff changeset
1152 </repeat>
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yating-l
parents: 18
diff changeset
1153 </repeat>
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yating-l
parents: 18
diff changeset
1154 <repeat name="group">
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yating-l
parents: 18
diff changeset
1155 <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
1156 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1157 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1158 <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
1159 <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
1160 <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
1161 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1162 </repeat>
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yating-l
parents: 18
diff changeset
1163 <repeat name="format">
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yating-l
parents: 18
diff changeset
1164 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1165 <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
1166 <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
1167 <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
1168 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1169 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1170 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1171 <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
1172 <!-- Check tracks exist -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1173 <!-- First group -->
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parents: 18
diff changeset
1174 <extra_files type="file"
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
1175 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
1176 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
1177 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1178 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1179 <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
1180 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
1181 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
1182 compare="sim_size"
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 <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
1185 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
1186 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
1187 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1188 />
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 <!-- Second group -->
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1191 <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
1192 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
1193 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
1194 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1195 />
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1196 <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
1197 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
1198 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
1199 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
1200 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
1201 <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
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parents: 18
diff changeset
1202 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1203 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1204
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1205 <!-- 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
1206 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1207 <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
1208 <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
1209 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1210 <param name="group_name" value="Default group"/>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1211 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1212 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1213 <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
1214 <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
1215 <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
1216 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1217 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1218 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1219 <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
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parents: 28
diff changeset
1220 <expand macro="verify_hub_structure" test="default_color" />
20
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parents: 18
diff changeset
1221 <!-- Verify trackDb.txt contains the color 0,0,0 -->
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
1222 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
20
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parents: 18
diff changeset
1223 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents: 18
diff changeset
1224 <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
1225 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1226 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1227
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1228 <!-- 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
1229 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1230 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1231
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1232 <!-- 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
1233 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1234 <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
1235 <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
1236 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1237 <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
1238 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1239 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1240 <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
1241 <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
1242 <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
1243 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1244 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1245 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1246 <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
1247 <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
1248 <!-- 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
1249 <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
1250 <assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1251 <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
1252 </assert_contents>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1253 </extra_files>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1254
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1255 <!-- 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
1256 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1257 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1258
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1259 <!-- 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
1260 <test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1261 <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
1262 <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
1263 <repeat name="group">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1264 <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
1265 <repeat name="format">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1266 <conditional name="formatChoice">
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1267 <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
1268 <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
1269 <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
1270 </conditional>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1271 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1272 </repeat>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1273 <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
1274 <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
1275 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
1276 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
1277 compare="sim_size"
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1278 />
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1279 <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
1280
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1281 <!-- 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
1282 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1283 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1284
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1285 <!-- 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
1286 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1287 <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
1288 <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
1289 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1290 <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
1291 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1292 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1293 <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
1294 <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
1295 <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
1296 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1297 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1298 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1299 <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
1300 <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
1301 <!-- 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
1302 <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
1303 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1304 <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
1305 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1306 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1307
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1308 <!-- 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
1309 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1310 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1311
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1312 <!-- 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
1313 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1314 <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
1315 <param name="fasta_file" value="common/dbia3.fa"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents: 28
diff changeset
1316 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1317 <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
1318 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1319 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1320 <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
1321 <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
1322 <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
1323 <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
1324 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1325 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1326 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1327 <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
1328 <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
1329 <!-- 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
1330 <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
1331 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1332 <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
1333 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1334 </extra_files>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1335
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1336 <!-- 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
1337 </output>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1338 </test>
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1339
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1340 <!-- 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
1341 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1342 <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
1343 <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
1344 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1345 <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
1346 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1347 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1348 <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
1349 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1350 <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
1351 <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
1352 <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
1353 <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
1354 <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
1355 <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
1356 <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
1357 <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
1358 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1359 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1360 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1361 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1362 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1363 <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
1364 <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
1365 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1366 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
1367 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
1368 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1369 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1370 <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
1371 <!-- 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
1372 <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
1373 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1374 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1375 <has_text text="searchTrix"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1376 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1377 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1378 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1379 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1380 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1381 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1382 <!-- check Trix index directory -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1383 <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
1384 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
1385 <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
1386 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
1387 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1388 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1389
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1390 <!-- 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
1391 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1392 <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
1393 <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
1394 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1395 <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
1396 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1397 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1398 <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
1399 <conditional name="bedChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1400 <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
1401 <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
1402 <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
1403 <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
1404 <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
1405 <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
1406 <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
1407 <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
1408 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1409 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1410 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1411 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1412 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1413 <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
1414 <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
1415 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1416 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
1417 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
1418 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1419 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1420 <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
1421 <!-- 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
1422 <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
1423 <assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1424 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1425 <has_text text="searchTrix"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1426 <has_text text="url"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1427 <has_text text="urlLabel"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1428 <has_text text="iframeUrl"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1429 <has_text text="iframeOptions"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1430 </assert_contents>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1431 </extra_files>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1432 <!-- check Trix index directory -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1433 <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
1434 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
1435 <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
1436 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
1437 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1438 </test>
20
40469b265ddb planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents: 18
diff changeset
1439
29
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1440 <!-- Test TrixIndex for BigBed -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1441 <test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1442 <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
1443 <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
1444 <repeat name="group">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1445 <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
1446 <repeat name="format">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1447 <conditional name="formatChoice">
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1448 <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
1449 <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
1450 <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
1451 <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
1452 <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
1453 <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
1454 <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
1455 <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
1456 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1457 </conditional>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1458 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1459 </repeat>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1460 <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
1461 <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
1462 <extra_files type="file"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1463 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
1464 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
1465 compare="sim_size"
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1466 />
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1467 <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
1468 <has_text text="searchIndex"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1469 <has_text text="searchTrix"/>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1470 </expand>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1471
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1472 <!-- check Trix index directory -->
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1473 <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
1474 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
1475 <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
1476 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
1477 </output>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1478 </test>
7e8a8b732db3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 28
diff changeset
1479
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1480 </tests>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1481
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1482 <help>
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1483 This Galaxy tool permits to prepare your files to be ready for
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1484 Assembly Hub visualization.
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1485 </help>
24
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1486
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1487 <citations>
fcc1021bd496 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 23
diff changeset
1488 <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
1489 </citations>
0
0f3bc17e5ede Uploaded
rmarenco
parents:
diff changeset
1490 </tool>