annotate hubArchiveCreator.xml @ 13:25809f699cb3 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children cbd8982c9f51
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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 <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="332">ucsc-bedtobigbed</requirement>
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15 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
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16 <requirement type="package" version="324">ucsc-genepredtobed</requirement>
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17 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
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18 <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
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19 <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
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20 <requirement type="package" version="324">ucsc-twobitinfo</requirement>
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21 <requirement type="package" version="1.3.1">samtools</requirement>
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22 </requirements>
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23
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24 <stdio>
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25 <regex match="^pass1"
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26 source="stderr"
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27 level="log"
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28 description="bedToBigBed"/>
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29 <!-- TODO: Add the case pass1 and 0 chroms -->
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30 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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31 </stdio>
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32
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33 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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34 <command detect_errors="exit_code"><![CDATA[
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35 mkdir -p $output.extra_files_path;
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36 python $__tool_directory__/hubArchiveCreator.py
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37
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38 ## Ask the user to enter the genome name
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39 --genome_name '$genome_name'
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40
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41 #import json
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42
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43 #set global data_parameter_dict = {}
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44
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45 ## Function to retrieve the data of the inputs
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46 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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47 #set false_path = str($input_to_prepare)
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48 #set name = $input_to_prepare.name
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49
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50 #set data_dict = {"name": $name}
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51 #silent data_dict.update($extra_data_dict)
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52
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53 ## Add the ordering by taking the tool form indexes
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54 #silent $data_dict.update({"order_index": $order_index + 1})
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55
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56 #silent $data_parameter_dict.update({$false_path: $data_dict})
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57
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58 #end def
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59
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60 #for $i, $f in enumerate( $format )
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61 #if $f.formatChoice.format_select == "bam"
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62 --bam $f.formatChoice.BAM
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63 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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64 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index})
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65 #end if
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66 #if $f.formatChoice.format_select == "bed"
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67 #if $f.formatChoice.bedChoice.bed_select == "bed"
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68 --bed $f.formatChoice.bedChoice.BED
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69 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i)
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70 #end if
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71 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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72 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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73 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i)
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74 #end if
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75 #end if
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76 #if $f.formatChoice.format_select == "bigwig"
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77 --bigwig $f.formatChoice.BIGWIG
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78 #silent $prepare_json($f.formatChoice.BIGWIG, $i)
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79 #end if
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80 #if $f.formatChoice.format_select == "gff3"
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81 --gff3 $f.formatChoice.GFF3
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82 #silent $prepare_json($f.formatChoice.GFF3, $i)
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83 #end if
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84 #if $f.formatChoice.format_select == "gtf"
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85 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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86 --gtf $f.formatChoice.GTF
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87 #silent $prepare_json($f.formatChoice.GTF, $i)
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88 #end if
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89 #end for
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90
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91 ## We combine the fasta file dataset name with his false path in a JSON object
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92 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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93 -f '$fasta_json'
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94
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95 ## Dump the final json
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96 #set all_data_json = json.dumps($data_parameter_dict)
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97
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98 --data_json '$all_data_json'
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99
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100 ## Retrieve the user email
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101 --user_email $__user_email__
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102
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103 -d $__tool_directory__
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104
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105 -e $output.files_path
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106
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107 $advanced_options.debug_mode
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108
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109 -o $output;
0
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110 ]]></command>
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111
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112 <inputs>
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113 <param
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114 name="genome_name"
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115 type="text"
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116 size="30"
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117 value="unknown"
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118 label="UCSC Genome Browser assembly ID"
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119 />
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120 <param
0
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121 format="fasta"
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122 name="fasta_file"
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123 type="data"
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124 label="Reference genome"
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125 />
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126 <repeat name="format" title="Formats">
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127 <conditional name="formatChoice">
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128 <param name="format_select" type="select" label="Format">
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129 <option value="bam" selected="true">BAM</option>
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130 <option value="bed">BED</option>
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131 <option value="bigwig">BIGWIG</option>
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132 <option value="gff3">GFF3</option>
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133 <option value="gtf">GTF</option>
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134 </param>
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135
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136 <when value="bam">
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137 <param
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138 format="bam"
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139 name="BAM"
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140 type="data"
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141 label="BAM File"
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142 />
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143 </when>
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144 <when value="bigwig">
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145 <param
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146 format="bigwig"
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147 name="BIGWIG"
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148 type="data"
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149 label="BIGWIG File"
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150 />
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151 </when>
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152 <when value="gff3">
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153 <param
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154 format="gff3"
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155 name="GFF3"
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156 type="data"
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157 label="GFF3 File"
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158 />
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159 </when>
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160 <when value="gtf">
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161 <param
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162 format="gtf"
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163 name="GTF"
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164 type="data"
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165 label="GTF File"
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166 />
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167 </when>
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168 <when value="bed">
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169 <conditional name="bedChoice">
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170 <param name="bed_select" type="select" label="Bed Choice">
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171 <option value="bed" selected="true">BED Generic (bed3+)</option>
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172 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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173 </param>
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174 <when value="bed">
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175 <param
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176 format="bed"
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177 name="BED"
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178 type="data"
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179 label="Generic Bed File Choice"
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180 />
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181 </when>
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182 <when value="bed_simple_repeats_option">
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183 <param
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184 format="bed"
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185 name="BED_simple_repeats"
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186 type="data"
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187 label="Bed Simple Repeats (Bed4+12) File"
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188 />
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189 </when>
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190 </conditional>
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191 </when>
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192 </conditional>
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193 </repeat>
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194 <conditional name="advanced_options">
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195 <param name="advanced_options_selector" type="select" label="Advanced options">
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196 <option value="off" selected="true">Hide advanced options</option>
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197 <option value="on">Display advanced options</option>
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198 </param>
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199 <!-- TODO: Avoid redundancy here -->
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200 <when value="on">
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201 <param name="debug_mode" type="boolean"
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202 label="Activate debug mode" checked="false"
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203 truevalue="--debug_mode" falsevalue="">
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204 <help>
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205 Use this option if you are a G-OnRamp developer
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206 </help>
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207 </param>
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208 </when>
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209 <when value="off">
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210 <param name="debug_mode" type="hidden"
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211 value="">
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212 </param>
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213 </when>
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214 </conditional>
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215 </inputs>
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216
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217 <outputs>
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218 <data format="trackhub" name="output"/>
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219 </outputs>
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220
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221 <tests>
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222 <!-- Can also use assert_command to test command -->
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223 <!-- Testing GFF3 input -->
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224 <test>
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225 <param name="fasta_file" value="dbia3.fa"/>
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226 <repeat name="format">
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227 <conditional name="formatChoice">
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228 <param name="format_select" value="gff3"/>
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229 <param name="GFF3" value="augustusDbia3.gff3"/>
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230 </conditional>
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231 </repeat>
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232 <repeat name="format">
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233 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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234 <!-- TODO: Ask why the tests are not passing with this xml:
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235 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history'
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236 <conditional name="formatChoice">
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237 <param name="format_select" value="bed"/>
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238 <conditional name="bedChoice">
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239 <param name="bed_select" value="bed_simple_repeats_option"/>
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240 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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241 </conditional>
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242 </conditional>
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243 -->
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244 </repeat>
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245
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246 <output name="output">
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247 <assert_contents>
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248 <has_text text="myHub"/>
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249 </assert_contents>
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250 <assert_contents>
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251 <has_text text="dbia3_trfBig.bb"/>
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252 </assert_contents>
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253 <assert_contents>
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254 <has_text text="SAODOAii qwwqod92921"/>
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255 </assert_contents>
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256 </output>
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257 </test>
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258 <test>
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259 <param name="fasta_file" value="dbia3.fa"/>
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260 <param name="GFF3" value="augustusDbia3.gff3"/>
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261 <output name="output" file="augustusOutput.html" lines_diff="2">
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262 <extra_files type="directory" value="myHub"/>
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263 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/>
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264 </output>
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265 </test>
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266 <!-- Testing Generic BED input -->
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267 <!-- Testing Bed Simple repeat input -->
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268 </tests>
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269
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270 <help>
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271 This Galaxy tool permits to prepare your files to be ready for
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272 Assembly Hub visualization.
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273 </help>
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274 </tool>