Mercurial > repos > yating-l > hubarchivecreator

annotate tests.xml @ 84:cb62314a6297 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Fri, 03 Nov 2017 17:08:19 -0400
parents
children a65e52152476
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84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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1 <macro>
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2 <xml name="test_cases">
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3 <!-- Test with only the fasta file -->
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4 <test>
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5 <param name="genome_name" value="Dbia3"/>
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6 <param name="fasta_file" value="common/dbia3.fa"/>
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7 <output name="output" file="only_genome/only_genome.html">
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8 <!-- Use macro to check the whole common structure without repeated code -->
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9 <expand macro="verify_hub_structure_no_track" test="only_genome" />
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10 </output>
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11 </test>
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12
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13 <!-- Test with Bam -->
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14 <test>
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15 <param name="genome_name" value="Dbia3"/>
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16 <param name="fasta_file" value="common/dbia3.fa"/>
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17 <repeat name="group">
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18 <param name="group_name" value="Default group"/>
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19 <repeat name="format">
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20 <conditional name="formatChoice">
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21 <param name="format_select" value="bam"/>
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22 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
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23 <param name="longLabel" value="HISAT sequence alignment" />
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24 <param name="track_color" value="#000000"/>
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25 </conditional>
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26 </repeat>
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27 </repeat>
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28 <output name="output" file="bam/bam.html">
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29 <!-- Verify tracks folder contains bam and bai -->
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30 <extra_files type="file"
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31 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
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32 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
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33 compare="sim_size"
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34 />
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35 <extra_files type="file"
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36 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
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37 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
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38 compare="sim_size"
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39 />
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40 <!-- Use macro to check the whole common structure without repeated code -->
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41 <expand macro="verify_hub_structure" test="bam" />
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42 </output>
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43 </test>
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44
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45 <!-- Test with Bed Generic -->
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46 <test>
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47 <param name="genome_name" value="Dbia3"/>
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48 <param name="fasta_file" value="common/dbia3.fa"/>
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49 <repeat name="group">
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50 <param name="group_name" value="Default group"/>
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51 <repeat name="format">
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52 <conditional name="formatChoice">
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53 <param name="format_select" value="bed" />
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54 <conditional name="bedChoice">
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55 <param name="bed_select" value="bed_generic"/>
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56 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
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57 <param name="longLabel" value="TBLASTN alignment" />
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58 <param name="track_color" value="#000000"/>
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59 </conditional>
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60 </conditional>
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61 </repeat>
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62 </repeat>
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63 <output name="output" file="bed_generic/bed_generic.html">
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64 <extra_files type="file"
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65 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
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66 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
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67 compare="sim_size"
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68 />
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69 <expand macro="verify_hub_structure" test="bed_generic" />
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70 </output>
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71 </test>
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72
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73 <!-- Test with Bed Simple repeat -->
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74 <test>
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75 <param name="genome_name" value="Dbia3"/>
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76 <param name="fasta_file" value="common/dbia3.fa"/>
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77 <repeat name="group">
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78 <param name="group_name" value="Default group"/>
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79 <repeat name="format">
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80 <conditional name="formatChoice">
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81 <param name="format_select" value="bed" />
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82 <conditional name="bedChoice">
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83 <param name="bed_select" value="bed_simple_repeats_option"/>
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84 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
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85 <param name="longLabel" value="Simple repeat" />
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86 <param name="track_color" value="#000000"/>
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87 </conditional>
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88 </conditional>
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89 </repeat>
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90 </repeat>
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91 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
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92 <extra_files type="file"
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93 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
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94 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
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95 compare="sim_size"
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96 />
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97 <expand macro="verify_hub_structure" test="bed_simple_repeats" />
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98 </output>
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99 </test>
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100
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101 <!-- Test with Psl -->
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102 <test>
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103 <param name="genome_name" value="Dbia3"/>
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104 <param name="fasta_file" value="common/dbia3.fa"/>
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105 <repeat name="group">
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106 <param name="group_name" value="Default group"/>
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107 <repeat name="format">
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108 <conditional name="formatChoice">
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109 <param name="format_select" value="psl"/>
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110 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
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111 <param name="longLabel" value="BLAST Alignment" />
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112 <param name="track_color" value="#000000"/>
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113 </conditional>
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114 </repeat>
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115 </repeat>
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116 <output name="output" file="psl/psl_trackhub.html">
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117 <extra_files type="file"
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118 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
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119 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
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120 compare="sim_size"
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121 />
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122 <expand macro="verify_hub_structure" test="psl" />
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123 </output>
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124 </test>
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125
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126 <!-- Test with BigWig -->
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127 <test>
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128 <param name="genome_name" value="Dbia3"/>
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129 <param name="fasta_file" value="common/dbia3.fa"/>
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130 <repeat name="group">
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131 <param name="group_name" value="Default group"/>
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132 <repeat name="format">
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133 <conditional name="formatChoice">
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134 <param name="format_select" value="bigwig"/>
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135 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
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136 <param name="longLabel" value="RNA-Seq Coverage" />
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137 <param name="track_color" value="#000000"/>
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138 </conditional>
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139 </repeat>
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140 </repeat>
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141 <output name="output" file="bigwig/bigwig.html">
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142 <extra_files type="file"
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143 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
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144 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
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145 compare="sim_size"
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146 />
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147 <expand macro="verify_hub_structure" test="bigwig" />
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148 <!-- check additional trackDb settings for BigWig -->
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149 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
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150 <assert_contents>
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151 <has_text text="autoScale"/>
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152 <has_text text="maxHeightPixels"/>
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153 <has_text text="windowingFunction"/>
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154 </assert_contents>
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155 </extra_files>
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156 </output>
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157 </test>
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158
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159 <!-- Test with GFF3 -->
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160 <test>
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161 <param name="genome_name" value="Dbia3"/>
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162 <param name="fasta_file" value="common/dbia3.fa"/>
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163 <repeat name="group">
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164 <param name="group_name" value="Default group"/>
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165 <repeat name="format">
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166 <conditional name="formatChoice">
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167 <param name="format_select" value="gff3"/>
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168 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
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169 <param name="longLabel" value="Augustus" />
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170 <param name="track_color" value="#000000"/>
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171 </conditional>
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172 </repeat>
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173 </repeat>
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174 <output name="output" file="gff3/gff3_trackhub.html">
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175 <extra_files type="file"
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176 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
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177 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
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178 compare="sim_size"
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179 />
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180 <expand macro="verify_hub_structure" test="gff3" />
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181 </output>
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182 </test>
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183
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184 <!-- Test with GTF -->
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185 <test>
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186 <param name="genome_name" value="Dbia3"/>
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187 <param name="fasta_file" value="common/dbia3.fa"/>
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188 <repeat name="group">
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189 <param name="group_name" value="Default group"/>
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190 <repeat name="format">
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191 <conditional name="formatChoice">
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192 <param name="format_select" value="gtf"/>
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193 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
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194 <param name="longLabel" value="StringTie transcripts" />
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195 <param name="track_color" value="#000000"/>
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196 </conditional>
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197 </repeat>
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198 </repeat>
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199 <output name="output" file="gtf/gtf_trackhub.html">
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200 <extra_files type="file"
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201 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
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202 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
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203 compare="sim_size"
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204 />
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205 <expand macro="verify_hub_structure" test="gtf" />
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206 </output>
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207 </test>
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208
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209 <!-- Test with BLAT Alignment -->
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210 <test>
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211 <param name="genome_name" value="Dbia3"/>
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212 <param name="fasta_file" value="common/dbia3.fa"/>
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213 <repeat name="group">
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214 <param name="group_name" value="Default group"/>
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215 <repeat name="format">
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216 <conditional name="formatChoice">
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217 <param name="format_select" value="bed" />
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218 <conditional name="bedChoice">
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219 <param name="bed_select" value="bed_blat_alignment_option"/>
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220 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
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221 <param name="longLabel" value="BLAT alignment" />
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222 <param name="track_color" value="#000000"/>
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223 <param name="database" value="NCBI" />
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224 </conditional>
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225 </conditional>
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226 </repeat>
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227 </repeat>
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228 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
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229 <extra_files type="file"
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230 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
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231 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
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232 compare="sim_size"
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233 />
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234 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
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235 <!-- check additional trackDb settings for BLAT -->
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236 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
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237 <assert_contents>
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238 <has_text text="searchIndex"/>
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239 <has_text text="url"/>
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240 <has_text text="urlLabel"/>
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241 <has_text text="iframeUrl"/>
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242 <has_text text="iframeOptions"/>
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243 </assert_contents>
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244 </extra_files>
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245 </output>
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246 </test>
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247
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248 <!-- Test with BLAST Alignment -->
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249 <test>
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250 <param name="genome_name" value="Dbia3"/>
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251 <param name="fasta_file" value="common/dbia3.fa"/>
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252 <repeat name="group">
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253 <param name="group_name" value="Default group"/>
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254 <repeat name="format">
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255 <conditional name="formatChoice">
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256 <param name="format_select" value="bed" />
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257 <conditional name="bedChoice">
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258 <param name="bed_select" value="bed_blast_alignment_option"/>
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259 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
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260 <param name="longLabel" value="BLAST alignment" />
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261 <param name="track_color" value="#000000"/>
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262 <param name="database" value="NCBI" />
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263 </conditional>
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264 </conditional>
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265 </repeat>
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266 </repeat>
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267 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
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268 <extra_files type="file"
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269 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
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270 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
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271 compare="sim_size"
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272 />
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273 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
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274 <!-- check additional trackDb settings for BLAST -->
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275 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
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276 <assert_contents>
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277 <has_text text="searchIndex"/>
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278 <has_text text="url"/>
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279 <has_text text="urlLabel"/>
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280 <has_text text="iframeUrl"/>
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281 <has_text text="iframeOptions"/>
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282 </assert_contents>
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283 </extra_files>
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284 </output>
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285 </test>
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286
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287 <!-- Test with Regtools Splice Junctions -->
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288 <test>
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289 <param name="genome_name" value="Dbia3"/>
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290 <param name="fasta_file" value="common/dbia3.fa"/>
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291 <repeat name="group">
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292 <param name="group_name" value="Default group"/>
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293 <repeat name="format">
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294 <conditional name="formatChoice">
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295 <param name="format_select" value="bed" />
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296 <conditional name="bedChoice">
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297 <param name="bed_select" value="bed_splice_junctions_option"/>
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298 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
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299 <param name="longLabel" value="Splice junctions" />
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300 <param name="track_color" value="#000000"/>
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301 </conditional>
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302 </conditional>
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303 </repeat>
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304 </repeat>
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305 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
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306 <extra_files type="file"
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307 name="myHub/Dbia3/tracks/regtools_junctions.bb"
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308 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
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309 compare="sim_size"
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310 />
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311 <expand macro="verify_hub_structure" test="bed_splice_junctions" />
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312 </output>
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313 </test>
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314
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315 <!-- Test with Cytoband -->
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316 <test>
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317 <param name="genome_name" value="Dbia3"/>
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318 <param name="fasta_file" value="common/dbia3.fa"/>
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319 <repeat name="group">
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320 <param name="group_name" value="Default group"/>
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321 <repeat name="format">
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322 <conditional name="formatChoice">
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323 <param name="format_select" value="bed" />
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324 <conditional name="bedChoice">
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325 <param name="bed_select" value="bed_cytoBand"/>
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326 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
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327 <param name="longLabel" value="Cytoband" />
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328 <param name="track_color" value="#000000"/>
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329 </conditional>
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330 </conditional>
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331 </repeat>
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332 </repeat>
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333 <output name="output" file="bed_cytoband/cytoband_trackhub.html">
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334 <extra_files type="file"
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335 name="myHub/Dbia3/tracks/Cytoband.bb"
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336 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
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337 compare="sim_size"
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338 />
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339 <expand macro="verify_hub_structure" test="bed_cytoband" />
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340 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
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341 <assert_contents>
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342 <has_text text="track cytoBandIdeo"/>
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343 </assert_contents>
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344 </extra_files>
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345 </output>
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346 </test>
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347
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348 <!-- Test with bigBed -->
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349 <test>
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350 <param name="genome_name" value="Dbia3"/>
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351 <param name="fasta_file" value="common/dbia3.fa"/>
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352 <repeat name="group">
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353 <param name="group_name" value="Default group"/>
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354 <repeat name="format">
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355 <conditional name="formatChoice">
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356 <param name="format_select" value="bigbed"/>
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357 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
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358 <param name="longLabel" value="bigBed" />
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359 <param name="track_color" value="#000000"/>
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360 </conditional>
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361 </repeat>
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362 </repeat>
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363 <output name="output" file="big_bed/bigbed_trackhub.html">
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364 <extra_files type="file"
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365 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
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366 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
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367 compare="sim_size"
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368 />
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369 <expand macro="verify_hub_structure" test="big_bed" />
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370 </output>
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371 </test>
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372
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373 <!-- Test with one group and multiple tracks -->
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374 <test>
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375 <param name="genome_name" value="Dbia3"/>
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376 <param name="fasta_file" value="common/dbia3.fa"/>
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377 <repeat name="group">
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378 <param name="group_name" value="Default group"/>
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379 <repeat name="format">
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diff changeset
380 <conditional name="formatChoice">
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yating-l
parents:
diff changeset
381 <param name="format_select" value="gtf"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
382 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
383 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
384 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
385 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
386 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
387 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
388 <param name="format_select" value="gff3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
389 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
390 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
391 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
392 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
393 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
394 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
395 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
396 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
397 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
398 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
399 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
400 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
401 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
402 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
403 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
404 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
405 <expand macro="verify_hub_structure" test="gtf_gff" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
406 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
407 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
408
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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parents:
diff changeset
409 <!-- Test with one group and all the supported datatypes -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
410 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
411 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
412 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
413 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
414 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
415 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
416 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
417 <param name="format_select" value="bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
418 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
419 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
420 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
421 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
422 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
423 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
424 <param name="format_select" value="bed"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
425 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
426 <param name="bed_select" value="bed_generic"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
427 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
428 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
429 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
430 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
431 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
432 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
433 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
434 <param name="format_select" value="bed"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
435 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
436 <param name="bed_select" value="bed_simple_repeats_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
437 <param name="BED_simple_repeats" ftype="bed"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
438 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
439 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
440 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
441 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
442 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
443 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
444 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
445 <param name="format_select" value="psl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
446 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
447 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
448 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
449 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
450 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
451 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
452 <param name="format_select" value="bigwig"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
453 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
454 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
455 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
456 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
457 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
458 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
459 <param name="format_select" value="gff3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
460 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
461 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
462 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
463 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
464 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
465 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
466 <param name="format_select" value="gtf"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
467 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
468 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
469 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
470 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
471 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
472 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
473 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
474 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
475 <param name="bed_select" value="bed_cytoBand"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
476 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
477 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
478 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
479 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
480 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
481 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
482 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
483 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
484 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
485 <param name="bed_select" value="bed_splice_junctions_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
486 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
487 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
488 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
489 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
490 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
491 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
492 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
493 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
494 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
495 <param name="bed_select" value="bed_blast_alignment_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
496 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
497 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
498 <param name="database" value="NCBI" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
499 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
500 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
501 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
502 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
503 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
504 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
505 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
506 <param name="bed_select" value="bed_blat_alignment_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
507 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
508 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
509 <param name="database" value="NCBI" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
510 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
511 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
512 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
513 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
514 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
515 <!-- verify tracks folder contains all the files -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
516 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
517 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
518 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
519 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
520 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
521 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
522 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
523 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
524 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
525 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
526 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
527 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
528 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
529 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
530 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
531 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
532 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
533 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
534 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
535 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
536 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
537 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
538 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
539 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
540 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
541 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
542 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
543 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
544 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
545 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
546 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
547 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
548 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
549 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
550 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
551 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
552 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
553 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
554 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
555 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
556 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
557 name="myHub/Dbia3/tracks/Cytoband.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
558 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
559 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
560 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
561 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
562 name="myHub/Dbia3/tracks/regtools_junctions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
563 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
564 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
565 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
566 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
567 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
568 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
569 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
570 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
571 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
572 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
573 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
574 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
575 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
576 <expand macro="verify_hub_structure" test="all_datatypes" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
577 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
578 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
579
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
580 <!-- Test with two groups and no tracks -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
581 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
582 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
583 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
584 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
585 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
586 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
587 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
588 <param name="group_name" value="Other group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
589 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
590 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
591 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
592 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
593 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
594
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
595 <!-- Test with two groups and one track in first -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
596 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
597 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
598 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
599 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
600 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
601 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
602 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
603 <param name="format_select" value="bigwig"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
604 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
605 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
606 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
607 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
608 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
609 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
610 <param name="group_name" value="Other group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
611 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
612 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
613 <!-- Check tracks exist -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
614 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
615 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
616 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
617 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
618 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
619 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
620 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
621 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
622
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
623 <!-- Test with two groups and one track in both -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
624 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
625 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
626 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
627 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
628 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
629 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
630 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
631 <param name="format_select" value="bigwig"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
632 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
633 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
634 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
635 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
636 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
637 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
638 <param name="group_name" value="Other group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
639 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
640 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
641 <param name="format_select" value="gtf"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
642 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
643 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
644 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
645 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
646 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
647 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
648 <!-- Check tracks exist -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
649 <!-- First group -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
650 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
651 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
652 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
653 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
654 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
655
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
656 <!-- Second group -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
657 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
658 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
659 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
660 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
661 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
662 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
663 <!-- Check the groups.txt exists and is properly populated -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
664 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
665 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
666
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
667 <!-- Test with two groups and multiple tracks in both -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
668 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
669 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
670 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
671 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
672 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
673 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
674 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
675 <param name="format_select" value="bigwig"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
676 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
677 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
678 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
679 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
680 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
681 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
682 <param name="format_select" value="bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
683 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
684 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
685 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
686 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
687 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
688 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
689 <param name="group_name" value="Other group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
690 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
691 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
692 <param name="format_select" value="gtf"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
693 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
694 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
695 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
696 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
697 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
698 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
699 <param name="format_select" value="gff3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
700 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
701 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
702 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
703 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
704 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
705 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
706 <!-- Check tracks exist -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
707 <!-- First group -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
708 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
709 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
710 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
711 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
712 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
713 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
714 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
715 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
716 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
717 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
718 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
719 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
720 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
721 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
722 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
723
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
724 <!-- Second group -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
725 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
726 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
727 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
728 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
729 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
730 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
731 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
732 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
733 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
734 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
735 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
736 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
737 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
738
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
739 <!-- Test default color in a track -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
740 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
741 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
742 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
743 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
744 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
745 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
746 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
747 <param name="format_select" value="bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
748 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
749 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
750 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
751 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
752 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
753 <output name="output" file="default_color/default_color_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
754 <expand macro="verify_hub_structure" test="default_color" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
755 <!-- Verify trackDb.txt contains the color 0,0,0 -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
756 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
757 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
758 <has_text text="color 0,0,0"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
759 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
760 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
761
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
762 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
763 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
764 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
765
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
766 <!-- Test changed color in a track -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
767 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
768 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
769 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
770 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
771 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
772 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
773 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
774 <param name="format_select" value="bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
775 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
776 <param name="track_color" value="#8064a2"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
777 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
778 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
779 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
780 <output name="output" file="changed_color/changed_color_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
781 <expand macro="verify_hub_structure" test="changed_color" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
782 <!-- Verify trackDb.txt contains the color 128,100,162 -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
783 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
784 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
785 <has_text text="color 128,100,162"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
786 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
787 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
788
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
789 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
790 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
791 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
792
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
793 <!-- Test for StringTie Chromosome end coordinates -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
794 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
795 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
796 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
797 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
798 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
799 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
800 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
801 <param name="format_select" value="gtf"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
802 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
803 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
804 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
805 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
806 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
807 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
808 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
809 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
810 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
811 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
812 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
813 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
814
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
815 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
816 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
817 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
818
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
819 <!-- Test default label in a track -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
820 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
821 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
822 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
823 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
824 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
825 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
826 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
827 <param name="format_select" value="bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
828 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
829 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
830 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
831 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
832 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
833 <output name="output" file="default_color/default_color_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
834 <expand macro="verify_hub_structure" test="default_color" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
835 <!-- Verify trackDb.txt contains default label -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
836 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
837 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
838 <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
839 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
840 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
841
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
842 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
843 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
844 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
845
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
846 <!-- Test customized label in a track -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
847 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
848 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
849 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
850 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
851 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
852 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
853 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
854 <param name="format_select" value="bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
855 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
856 <param name="longLabel" value="HISAT sequence alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
857 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
858 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
859 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
860 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
861 <output name="output" file="changed_label/changed_label_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
862 <expand macro="verify_hub_structure" test="changed_label" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
863 <!-- Verify trackDb.txt contains the customized label -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
864 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
865 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
866 <has_text text="longLabel HISAT sequence alignment"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
867 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
868 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
869
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
870 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
871 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
872 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
873
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
874 <!-- Test TrixIndex for Blat alignment track -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
875 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
876 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
877 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
878 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
879 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
880 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
881 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
882 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
883 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
884 <param name="bed_select" value="bed_blat_alignment_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
885 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
886 <param name="longLabel" value="BLAT alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
887 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
888 <param name="database" value="NCBI" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
889 <conditional name="add_trix_index">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
890 <param name="add_trix_index_selector" value="yes" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
891 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
892 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
893 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
894 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
895 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
896 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
897 <param name="debug_mode" value="true" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
898 <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
899 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
900 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
901 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
902 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
903 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
904 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
905 <!-- check additional trackDb settings for BLAT -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
906 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
907 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
908 <has_text text="searchIndex"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
909 <has_text text="searchTrix"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
910 <has_text text="url"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
911 <has_text text="urlLabel"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
912 <has_text text="iframeUrl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
913 <has_text text="iframeOptions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
914 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
915 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
916 <!-- check Trix index directory -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
917 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
918 value="trix_index/blat_out.ix" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
919 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
920 value="trix_index/blat_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
921 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
922 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
923
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
924 <!-- Test TrixIndex for BLAST Alignment -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
925 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
926 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
927 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
928 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
929 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
930 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
931 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
932 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
933 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
934 <param name="bed_select" value="bed_blast_alignment_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
935 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
936 <param name="longLabel" value="BLAST alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
937 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
938 <param name="database" value="NCBI" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
939 <conditional name="add_trix_index">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
940 <param name="add_trix_index_selector" value="yes" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
941 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
942 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
943 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
944 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
945 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
946 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
947 <param name="debug_mode" value="true" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
948 <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
949 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
950 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
951 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
952 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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parents:
diff changeset
953 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
954 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
955 <!-- check additional trackDb settings for BLAST -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
956 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
957 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
958 <has_text text="searchIndex"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
959 <has_text text="searchTrix"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
960 <has_text text="url"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
961 <has_text text="urlLabel"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
962 <has_text text="iframeUrl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
963 <has_text text="iframeOptions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
964 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
965 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
966 <!-- check Trix index directory -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
967 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
968 value="trix_index/blast_out.ix" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
969 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
970 value="trix_index/blast_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
971 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
972 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
973
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
974 <!-- Test TrixIndex for BigBed -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
975 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
976 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
977 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
978 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
979 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
980 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
981 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
982 <param name="format_select" value="bigbed"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
983 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
984 <param name="longLabel" value="bigBed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
985 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
986 <conditional name="add_trix_index">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
987 <param name="add_trix_index_selector" value="yes" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
988 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
989 <param name="trix_id" value="name" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
990 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
991 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
992 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
993 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
994 <param name="debug_mode" value="true" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
995 <output name="output" file="trix_index_files/bigbed_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
996 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
997 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
998 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
999 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1000 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1001 <expand macro="verify_hub_structure" test="big_bed">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1002 <has_text text="searchIndex"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1003 <has_text text="searchTrix"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1004 </expand>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1005
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1006 <!-- check Trix index directory -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1007 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1008 value="trix_index/blat_out.ix" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1009 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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diff changeset
1010 value="trix_index/blat_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1011 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
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1012 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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parents:
diff changeset
1013
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1014 <!-- Test for big files? -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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parents:
diff changeset
1015
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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parents:
diff changeset
1016 <!-- Find tests that should fail -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents:
diff changeset
1017 </xml>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
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1018 </macro>