Mercurial > repos > rmarenco > hubarchivecreator

annotate hubArchiveCreator.xml @ 18:d786bca6a75d draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3007f4ce1d6e8ac8324970d355f028b9394e2a5f
author rmarenco
date Fri, 30 Sep 2016 18:33:03 -0400
parents c02720d1afee
children 40469b265ddb
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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
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2 <description>
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3 This Galaxy tool permits to prepare your files to be ready for
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4 Assembly Hub visualization.
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5 </description>
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6
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7 <requirements>
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8 <!-- Conda dependencies -->
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9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
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10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
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11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>
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12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
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13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
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14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
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15 <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
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16 <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
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17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
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18 <requirement type="package" version="1.3">samtools</requirement>
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19 <!-- ToolShed dependencies -->
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20 <requirement type="package" version="312">ucsc_tools</requirement>
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21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
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22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
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23 <requirement type="package" version="0.0.1">genePredToBed</requirement>
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24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
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25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
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26 <requirement type="package" version="1.2">samtools</requirement>
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27 </requirements>
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28
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29 <stdio>
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30 <regex match="^pass1"
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31 source="stderr"
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32 level="log"
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33 description="bedToBigBed"/>
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34 <!-- TODO: Add the case pass1 and 0 chroms -->
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35 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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36 </stdio>
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37
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38 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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39 <command detect_errors="exit_code"><![CDATA[
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40 mkdir -p $output.extra_files_path;
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41 python $__tool_directory__/hubArchiveCreator.py
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42
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43 ## Ask the user to enter the genome name
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44 --genome_name '$genome_name'
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45
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46 #import json
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47
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48 #set global data_parameter_dict = {}
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49
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50 ## Function to retrieve the data of the inputs
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51 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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52 #set false_path = str($input_to_prepare)
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53 #set name = $input_to_prepare.name
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54
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55 #set data_dict = {"name": $name}
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56 #silent data_dict.update($extra_data_dict)
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57
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58 ## Add the ordering by taking the tool form indexes
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59 #silent $data_dict.update({"order_index": $order_index})
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61 #silent $data_parameter_dict.update({$false_path: $data_dict})
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62
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63 #end def
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66 ## Get the number of digits from tracks, to have a unique integer from group index and track index
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68 #set temp_max_digit = 0
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70 #for $g in $group
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71 #if len($g.format) > $temp_max_digit
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72 #silent temp_max_digit = len($g.format)
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73 #end if
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74 #end for
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76 #set nb_digits_max_track = len(str($temp_max_digit))
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78 ## END Get the number of digits
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79
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80 #for $i_g, $g in enumerate( $group )
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81 #for $i, $f in enumerate( $g.format )
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82 ## Create the order index using index_group+1 concatenated with index_track
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83 #set index_group_final = str($i_g + 1)
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84 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
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86 ## For each format, we have a few mandatory fields we store in a dict
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87 #set track_color = str($f.formatChoice.track_color)
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88 #set group_name = str($g.group_name)
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89
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90 #set extra_data_dict = {"track_color": $track_color,
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91 "group_name": $group_name}
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93 #if $f.formatChoice.format_select == "bam"
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94 --bam $f.formatChoice.BAM
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95 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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97 ## Add Bam format specific fields
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98 #silent extra_data_dict.update({"index": $bam_index})
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99
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100 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
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101 #end if
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102 #if $f.formatChoice.format_select == "bed"
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103 #if $f.formatChoice.bedChoice.bed_select == "bed"
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104 --bed $f.formatChoice.bedChoice.BED
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105 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
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106 extra_data_dict)
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107 #end if
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108 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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109 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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110 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
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111 extra_data_dict)
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112 #end if
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113 #end if
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114 #if $f.formatChoice.format_select == "psl"
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115 --psl $f.formatChoice.PSL
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116 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
17
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117 extra_data_dict)
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118 #end if
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119 #if $f.formatChoice.format_select == "bigwig"
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120 --bigwig $f.formatChoice.BIGWIG
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121 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
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122 extra_data_dict)
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123 #end if
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124 #if $f.formatChoice.format_select == "gff3"
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125 --gff3 $f.formatChoice.GFF3
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126 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
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127 extra_data_dict)
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128 #end if
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129 #if $f.formatChoice.format_select == "gtf"
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130 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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131 --gtf $f.formatChoice.GTF
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132 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
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133 extra_data_dict)
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134 #end if
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135 #end for
0
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136 #end for
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137
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138 ## We combine the fasta file dataset name with his false path in a JSON object
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139 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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140 -f '$fasta_json'
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141
0
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142 ## Dump the final json
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143 #set all_data_json = json.dumps($data_parameter_dict)
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144
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145 --data_json '$all_data_json'
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146
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147 ## Retrieve the user email
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148 --user_email $__user_email__
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149
13
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150 -d $__tool_directory__
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151
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152 -e $output.files_path
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153
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154 $advanced_options.debug_mode
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155
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156 -o $output;
0
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157 ]]></command>
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158
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159 <inputs>
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160 <param
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161 name="genome_name"
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162 type="text"
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163 size="30"
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164 value="unknown"
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165 label="UCSC Genome Browser assembly ID"
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166 />
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167 <param
0
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168 format="fasta"
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169 name="fasta_file"
0
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170 type="data"
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171 label="Reference genome"
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172 />
17
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173 <repeat name="group" title="New group">
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174 <param type="text" name="group_name" label="Group name" value="Default group"/>
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175 <repeat name="format" title="New track">
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176 <conditional name="formatChoice">
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177 <param name="format_select" type="select" label="Format">
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178 <option value="bam" selected="true">BAM</option>
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179 <option value="bed">BED</option>
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180 <option value="psl">PSL</option>
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181 <option value="bigwig">BIGWIG</option>
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182 <option value="gff3">GFF3</option>
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183 <option value="gtf">GTF</option>
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184 </param>
17
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185
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186 <when value="bam">
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187 <param
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188 format="bam"
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189 name="BAM"
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190 type="data"
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191 label="BAM File"
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192 />
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193 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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194 <param name="track_color" type="color" label="Track color" value="#000000">
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195 <sanitizer>
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196 <valid initial="string.letters,string.digits">
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197 <add value="#"/>
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198 </valid>
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199 </sanitizer>
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200 </param>
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201 </when>
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202 <when value="bed">
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203 <conditional name="bedChoice">
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204 <param name="bed_select" type="select" label="Bed Choice">
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205 <option value="bed" selected="true">BED Generic (bed3+)</option>
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206 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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207 </param>
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208 <when value="bed">
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209 <param
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210 format="bed"
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211 name="BED"
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212 type="data"
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213 label="Generic Bed File Choice"
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214 />
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215
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216 </when>
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rmarenco
parents: 16
diff changeset
217 <when value="bed_simple_repeats_option">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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parents: 16
diff changeset
218 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
219 format="bed"
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diff changeset
220 name="BED_simple_repeats"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
221 type="data"
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diff changeset
222 label="Bed Simple Repeats (Bed4+12) File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
223 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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224 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
225 </conditional>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
226 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
227 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
228 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
229 <add value="#"/>
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diff changeset
230 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
231 </sanitizer>
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diff changeset
232 </param>
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233 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
234 <when value="psl">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
235 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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236 format="psl"
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237 name="PSL"
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diff changeset
238 type="data"
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diff changeset
239 label="PSL File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
240 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
241 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
242 <sanitizer>
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diff changeset
243 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
244 <add value="#"/>
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diff changeset
245 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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246 </sanitizer>
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247 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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248 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
249 <when value="bigwig">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
250 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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251 format="bigwig"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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252 name="BIGWIG"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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253 type="data"
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254 label="BIGWIG File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
255 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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256 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
257 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
258 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
259 <add value="#"/>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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260 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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261 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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262 </param>
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263 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
264 <when value="gff3">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
265 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
266 format="gff3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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267 name="GFF3"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
268 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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269 label="GFF3 File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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270 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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271 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
272 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
273 <valid initial="string.letters,string.digits">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
274 <add value="#"/>
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275 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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276 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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277 </param>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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278 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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279 <when value="gtf">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
280 <param
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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281 format="gtf"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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282 name="GTF"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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283 type="data"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
284 label="GTF File"
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
285 />
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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286 <param name="track_color" type="color" label="Track color" value="#000000">
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
287 <sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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diff changeset
288 <valid initial="string.letters,string.digits">
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diff changeset
289 <add value="#"/>
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290 </valid>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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291 </sanitizer>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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292 </param>
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293 </when>
c02720d1afee planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
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294 </conditional>
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295 </repeat>
0
0f3bc17e5ede Uploaded
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diff changeset
296 </repeat>
13
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diff changeset
297 <conditional name="advanced_options">
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298 <param name="advanced_options_selector" type="select" label="Advanced options">
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299 <option value="off" selected="true">Hide advanced options</option>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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300 <option value="on">Display advanced options</option>
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301 </param>
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diff changeset
302 <!-- TODO: Avoid redundancy here -->
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diff changeset
303 <when value="on">
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304 <param name="debug_mode" type="boolean"
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305 label="Activate debug mode" checked="false"
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306 truevalue="--debug_mode" falsevalue="">
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307 <help>
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308 Use this option if you are a G-OnRamp developer
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309 </help>
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310 </param>
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311 </when>
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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diff changeset
312 <when value="off">
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313 <param name="debug_mode" type="hidden"
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diff changeset
314 value="">
25809f699cb3 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
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diff changeset
315 </param>
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316 </when>
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317 </conditional>
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318 </inputs>
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319
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320 <outputs>
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321 <data format="trackhub" name="output"/>
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322 </outputs>
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323
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324 <tests>
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325 <!-- Can also use assert_command to test command -->
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326 <!-- Testing GFF3 input -->
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327 <test>
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328 <param name="fasta_file" value="dbia3.fa"/>
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329 <repeat name="format">
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330 <conditional name="formatChoice">
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331 <param name="format_select" value="gff3"/>
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332 <param name="GFF3" value="augustusDbia3.gff3"/>
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333 </conditional>
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334 </repeat>
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335 <repeat name="format">
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336 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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337 <!-- TODO: Ask why the tests are not passing with this xml:
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338 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history'
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339 <conditional name="formatChoice">
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340 <param name="format_select" value="bed"/>
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341 <conditional name="bedChoice">
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342 <param name="bed_select" value="bed_simple_repeats_option"/>
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343 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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344 </conditional>
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345 </conditional>
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346 -->
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347 </repeat>
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348
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349 <output name="output">
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350 <assert_contents>
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351 <has_text text="myHub"/>
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352 </assert_contents>
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353 <assert_contents>
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354 <has_text text="dbia3_trfBig.bb"/>
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355 </assert_contents>
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356 <assert_contents>
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357 <has_text text="SAODOAii qwwqod92921"/>
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358 </assert_contents>
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359 </output>
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360 </test>
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361 <test>
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362 <param name="fasta_file" value="dbia3.fa"/>
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363 <param name="GFF3" value="augustusDbia3.gff3"/>
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364 <output name="output" file="augustusOutput.html" lines_diff="2">
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365 <extra_files type="directory" value="myHub"/>
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366 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/>
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367 </output>
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368 </test>
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369 <!-- Testing Generic BED input -->
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370 <!-- Testing Bed Simple repeat input -->
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371 </tests>
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372
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373 <help>
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374 This Galaxy tool permits to prepare your files to be ready for
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375 Assembly Hub visualization.
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376 </help>
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377 </tool>