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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.0.2">
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2 <description>
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3 This Galaxy tool permits to prepare your files to be ready for
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4 Assembly Hub visualization.
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5 </description>
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6
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7 <requirements>
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8 <requirement type="package" version="312">ucsc_tools</requirement>
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9 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
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10 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
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11 <requirement type="package" version="0.0.1">genePredToBed</requirement>
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12 <requirement type="package" version="1.2">samtools</requirement>
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13 <!-- Conda dependencies -->
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14 <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
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15 <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
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16 <requirement type="package" version="324">ucsc-genepredtobed</requirement>
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17 <requirement type="package" version="1.3.1">samtools</requirement>
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18 </requirements>
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19
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20 <stdio>
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21 <regex match="^pass1"
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22 source="stderr"
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23 level="log"
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24 description="bedToBigBed"/>
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25 <!-- TODO: Add the case pass1 and 0 chroms -->
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26 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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27 </stdio>
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28
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29 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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30 <command detect_errors="exit_code"><![CDATA[
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31 mkdir -p $output.extra_files_path;
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32 python $__tool_directory__/hubArchiveCreator.py
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33
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34 #import json
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35
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36 #set global data_parameter_dict = {}
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37
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38 ## Function to retrieve the data of the inputs
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39 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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40 #set false_path = str($input_to_prepare)
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41 #set name = $input_to_prepare.name
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42
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43 #set data_dict = {"name": $name}
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44 #silent data_dict.update($extra_data_dict)
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45
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46 ## Add the ordering by taking the tool form indexes
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47 #silent $data_dict.update({"order_index": $order_index + 1})
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48
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49 #silent $data_parameter_dict.update({$false_path: $data_dict})
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50
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51 #end def
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52
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53 #for $i, $f in enumerate( $format )
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54 #if $f.formatChoice.format_select == "bam"
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55 --bam $f.formatChoice.BAM
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56 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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57 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index})
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58 #end if
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59 #if $f.formatChoice.format_select == "bed"
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60 #if $f.formatChoice.bedChoice.bed_select == "bed"
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61 --bed $f.formatChoice.bedChoice.BED
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62 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i)
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63 #end if
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64 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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65 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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66 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i)
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67 #end if
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68 #end if
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69 #if $f.formatChoice.format_select == "bigwig"
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70 --bigwig $f.formatChoice.BIGWIG
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71 #silent $prepare_json($f.formatChoice.BIGWIG, $i)
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72 #end if
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73 #if $f.formatChoice.format_select == "gff3"
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74 --gff3 $f.formatChoice.GFF3
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75 #silent $prepare_json($f.formatChoice.GFF3, $i)
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76 #end if
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77 #if $f.formatChoice.format_select == "gtf"
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78 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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79 --gtf $f.formatChoice.GTF
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80 #silent $prepare_json($f.formatChoice.GTF, $i)
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81 #end if
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82 #end for
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83
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84 ## Dump the final json
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85 #set all_data_json = json.dumps($data_parameter_dict)
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86
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87 -f $Fasta_File
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88 --data_json '$all_data_json'
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89
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90 -d $__tool_directory__ -e $output.files_path -o $output;
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91 ]]></command>
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92
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93 <inputs>
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94 <param
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95 format="fasta"
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96 name="Fasta_File"
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97 type="data"
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98 label="Reference genome"
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99 />
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100 <repeat name="format" title="Formats">
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101 <conditional name="formatChoice">
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102 <param name="format_select" type="select" label="Format">
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103 <option value="bam" selected="true">BAM</option>
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104 <option value="bed">BED</option>
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105 <option value="bigwig">BIGWIG</option>
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106 <option value="gff3">GFF3</option>
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107 <option value="gtf">GTF</option>
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108 </param>
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109
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110 <when value="bam">
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111 <param
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112 format="bam"
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113 name="BAM"
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114 type="data"
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115 label="BAM File"
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116 />
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117 </when>
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118 <when value="bigwig">
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119 <param
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120 format="bigwig"
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121 name="BIGWIG"
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122 type="data"
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123 label="BIGWIG File"
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124 />
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125 </when>
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126 <when value="gff3">
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127 <param
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128 format="gff3"
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129 name="GFF3"
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130 type="data"
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131 label="GFF3 File"
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132 />
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133 </when>
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134 <when value="gtf">
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135 <param
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136 format="gtf"
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137 name="GTF"
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138 type="data"
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139 label="GTF File"
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140 />
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141 </when>
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142 <when value="bed">
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143 <conditional name="bedChoice">
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144 <param name="bed_select" type="select" label="Bed Choice">
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145 <option value="bed" selected="true">Generic BED</option>
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146 <option value="bed_simple_repeats_option">BED simple repeats</option>
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147 </param>
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148 <when value="bed">
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149 <param
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150 format="bed"
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151 name="BED"
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152 type="data"
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153 label="Generic Bed File Choice"
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154 />
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155 </when>
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156 <when value="bed_simple_repeats_option">
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157 <param
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158 format="bed"
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159 name="BED_simple_repeats"
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160 type="data"
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161 label="Bed Simple Repeats (Bed4+12) File"
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162 />
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163 </when>
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164 </conditional>
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165 </when>
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166 </conditional>
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167 </repeat>
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168 </inputs>
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169
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170 <outputs>
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171 <data format="trackhub" name="output"/>
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172 </outputs>
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173
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174 <tests>
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175 <!-- Can also use assert_command to test command -->
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176 <!-- Testing GFF3 input -->
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177 <test>
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178 <param name="Fasta_File" value="dbia3.fa"/>
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179 <repeat name="format">
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180 <conditional name="formatChoice">
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181 <param name="format_select" value="gff3"/>
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182 <param name="GFF3" value="augustusDbia3.gff3"/>
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183 </conditional>
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184 </repeat>
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185 <repeat name="format">
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186 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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187 <!-- TODO: Ask why the tests are not passing with this xml:
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188 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history'
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189 <conditional name="formatChoice">
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190 <param name="format_select" value="bed"/>
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191 <conditional name="bedChoice">
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192 <param name="bed_select" value="bed_simple_repeats_option"/>
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193 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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194 </conditional>
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195 </conditional>
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196 -->
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197 </repeat>
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198
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199 <output name="output">
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200 <assert_contents>
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201 <has_text text="myHub"/>
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202 </assert_contents>
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203 <assert_contents>
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204 <has_text text="dbia3_trfBig.bb"/>
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205 </assert_contents>
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206 <assert_contents>
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207 <has_text text="SAODOAii qwwqod92921"/>
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208 </assert_contents>
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209 </output>
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210 </test>
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211 <test>
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212 <param name="Fasta_File" value="dbia3.fa"/>
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213 <param name="GFF3" value="augustusDbia3.gff3"/>
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214 <output name="output" file="augustusOutput.html" lines_diff="2">
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215 <extra_files type="directory" value="myHub"/>
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216 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/>
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217 </output>
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218 </test>
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219 <!-- Testing Generic BED input -->
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220 <!-- Testing Bed Simple repeat input -->
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221 </tests>
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222
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223 <help>
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224 This Galaxy tool permits to prepare your files to be ready for
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225 Assembly Hub visualization.
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226 </help>
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227 </tool>
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