Mercurial > repos > rmarenco > hubarchivecreator

annotate hubArchiveCreator.xml @ 16:3233451a3bd6 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author rmarenco
date Sun, 25 Sep 2016 11:25:38 -0400
parents 2a45cd656e8e
children c02720d1afee
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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 <requirement type="package" version="332">ucsc-psltobigpsl</requirement>
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16 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
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17 <requirement type="package" version="1.3">samtools</requirement>
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18 <!-- ToolShed dependencies -->
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19 <requirement type="package" version="312">ucsc_tools</requirement>
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20 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
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21 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
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22 <requirement type="package" version="0.0.1">genePredToBed</requirement>
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23 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
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24 <requirement type="package" version="1.2">samtools</requirement>
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25 </requirements>
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26
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27 <stdio>
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28 <regex match="^pass1"
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29 source="stderr"
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30 level="log"
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31 description="bedToBigBed"/>
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32 <!-- TODO: Add the case pass1 and 0 chroms -->
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33 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
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34 </stdio>
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35
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36 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
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37 <command detect_errors="exit_code"><![CDATA[
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38 mkdir -p $output.extra_files_path;
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39 python $__tool_directory__/hubArchiveCreator.py
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40
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41 ## Ask the user to enter the genome name
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42 --genome_name '$genome_name'
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43
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44 #import json
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45
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46 #set global data_parameter_dict = {}
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47
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48 ## Function to retrieve the data of the inputs
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49 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
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50 #set false_path = str($input_to_prepare)
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51 #set name = $input_to_prepare.name
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52
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53 #set data_dict = {"name": $name}
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54 #silent data_dict.update($extra_data_dict)
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55
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56 ## Add the ordering by taking the tool form indexes
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57 #silent $data_dict.update({"order_index": $order_index + 1})
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58
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59 #silent $data_parameter_dict.update({$false_path: $data_dict})
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60
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61 #end def
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62
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63 #for $i, $f in enumerate( $format )
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64 #set track_color = str($f.formatChoice.track_color)
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65
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66 #if $f.formatChoice.format_select == "bam"
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67 --bam $f.formatChoice.BAM
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68 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
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69 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index,
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70 "track_color": $track_color})
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71 #end if
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72 #if $f.formatChoice.format_select == "bed"
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73 #if $f.formatChoice.bedChoice.bed_select == "bed"
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74 --bed $f.formatChoice.bedChoice.BED
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75 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i,
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76 {"track_color": $track_color})
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77 #end if
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78 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
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79 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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80 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i,
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81 {"track_color": $track_color})
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82 #end if
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83 #end if
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84 #if $f.formatChoice.format_select == "psl"
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85 --psl $f.formatChoice.PSL
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86 #silent $prepare_json($f.formatChoice.PSL, $i,
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87 {"track_color": $track_color})
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88 #end if
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89 #if $f.formatChoice.format_select == "bigwig"
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90 --bigwig $f.formatChoice.BIGWIG
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91 #silent $prepare_json($f.formatChoice.BIGWIG, $i,
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92 {"track_color": $track_color})
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93 #end if
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94 #if $f.formatChoice.format_select == "gff3"
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95 --gff3 $f.formatChoice.GFF3
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96 #silent $prepare_json($f.formatChoice.GFF3, $i,
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97 {"track_color": $track_color})
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98 #end if
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99 #if $f.formatChoice.format_select == "gtf"
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100 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
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101 --gtf $f.formatChoice.GTF
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102 #silent $prepare_json($f.formatChoice.GTF, $i,
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103 {"track_color": $track_color})
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104 #end if
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105 #end for
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106
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107 ## We combine the fasta file dataset name with his false path in a JSON object
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108 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
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109 -f '$fasta_json'
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110
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111 ## Dump the final json
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112 #set all_data_json = json.dumps($data_parameter_dict)
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113
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114 --data_json '$all_data_json'
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115
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116 ## Retrieve the user email
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117 --user_email $__user_email__
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118
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119 -d $__tool_directory__
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121 -e $output.files_path
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123 $advanced_options.debug_mode
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125 -o $output;
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126 ]]></command>
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127
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128 <inputs>
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129 <param
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130 name="genome_name"
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131 type="text"
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132 size="30"
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133 value="unknown"
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134 label="UCSC Genome Browser assembly ID"
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135 />
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136 <param
0
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137 format="fasta"
10
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138 name="fasta_file"
0
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139 type="data"
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140 label="Reference genome"
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141 />
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142 <repeat name="format" title="Formats">
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143 <conditional name="formatChoice">
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144 <param name="format_select" type="select" label="Format">
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145 <option value="bam" selected="true">BAM</option>
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146 <option value="bed">BED</option>
16
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147 <option value="psl">PSL</option>
0
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148 <option value="bigwig">BIGWIG</option>
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149 <option value="gff3">GFF3</option>
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150 <option value="gtf">GTF</option>
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151 </param>
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152
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153 <when value="bam">
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154 <param
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155 format="bam"
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156 name="BAM"
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157 type="data"
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158 label="BAM File"
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159 />
16
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160 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
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161 <param name="track_color" type="color" label="Track color" value="#000000">
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162 <sanitizer>
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163 <valid initial="string.letters,string.digits">
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164 <add value="#"/>
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165 </valid>
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166 </sanitizer>
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167 </param>
0
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168 </when>
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169 <when value="bed">
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170 <conditional name="bedChoice">
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171 <param name="bed_select" type="select" label="Bed Choice">
11
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172 <option value="bed" selected="true">BED Generic (bed3+)</option>
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173 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
0
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174 </param>
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175 <when value="bed">
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176 <param
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177 format="bed"
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178 name="BED"
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179 type="data"
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180 label="Generic Bed File Choice"
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181 />
16
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182
0
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183 </when>
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184 <when value="bed_simple_repeats_option">
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185 <param
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186 format="bed"
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187 name="BED_simple_repeats"
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188 type="data"
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189 label="Bed Simple Repeats (Bed4+12) File"
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190 />
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191 </when>
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192 </conditional>
16
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193 <param name="track_color" type="color" label="Track color" value="#000000">
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194 <sanitizer>
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195 <valid initial="string.letters,string.digits">
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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196 <add value="#"/>
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197 </valid>
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198 </sanitizer>
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diff changeset
199 </param>
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200 </when>
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201 <when value="psl">
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diff changeset
202 <param
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203 format="psl"
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204 name="PSL"
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205 type="data"
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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206 label="PSL File"
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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207 />
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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208 <param name="track_color" type="color" label="Track color" value="#000000">
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diff changeset
209 <sanitizer>
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diff changeset
210 <valid initial="string.letters,string.digits">
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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diff changeset
211 <add value="#"/>
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diff changeset
212 </valid>
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diff changeset
213 </sanitizer>
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diff changeset
214 </param>
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215 </when>
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diff changeset
216 <when value="bigwig">
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diff changeset
217 <param
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218 format="bigwig"
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219 name="BIGWIG"
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220 type="data"
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221 label="BIGWIG File"
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222 />
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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223 <param name="track_color" type="color" label="Track color" value="#000000">
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224 <sanitizer>
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diff changeset
225 <valid initial="string.letters,string.digits">
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diff changeset
226 <add value="#"/>
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227 </valid>
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228 </sanitizer>
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229 </param>
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230 </when>
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diff changeset
231 <when value="gff3">
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diff changeset
232 <param
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233 format="gff3"
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234 name="GFF3"
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235 type="data"
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236 label="GFF3 File"
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237 />
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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diff changeset
238 <param name="track_color" type="color" label="Track color" value="#000000">
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diff changeset
239 <sanitizer>
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diff changeset
240 <valid initial="string.letters,string.digits">
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diff changeset
241 <add value="#"/>
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diff changeset
242 </valid>
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diff changeset
243 </sanitizer>
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diff changeset
244 </param>
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diff changeset
245 </when>
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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diff changeset
246 <when value="gtf">
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diff changeset
247 <param
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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diff changeset
248 format="gtf"
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diff changeset
249 name="GTF"
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diff changeset
250 type="data"
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
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diff changeset
251 label="GTF File"
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252 />
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253 <param name="track_color" type="color" label="Track color" value="#000000">
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254 <sanitizer>
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255 <valid initial="string.letters,string.digits">
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256 <add value="#"/>
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257 </valid>
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258 </sanitizer>
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259 </param>
0
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260 </when>
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261 </conditional>
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262 </repeat>
13
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263 <conditional name="advanced_options">
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264 <param name="advanced_options_selector" type="select" label="Advanced options">
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265 <option value="off" selected="true">Hide advanced options</option>
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266 <option value="on">Display advanced options</option>
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267 </param>
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268 <!-- TODO: Avoid redundancy here -->
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269 <when value="on">
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270 <param name="debug_mode" type="boolean"
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271 label="Activate debug mode" checked="false"
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272 truevalue="--debug_mode" falsevalue="">
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273 <help>
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274 Use this option if you are a G-OnRamp developer
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275 </help>
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276 </param>
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277 </when>
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278 <when value="off">
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279 <param name="debug_mode" type="hidden"
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280 value="">
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281 </param>
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282 </when>
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283 </conditional>
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284 </inputs>
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285
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286 <outputs>
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287 <data format="trackhub" name="output"/>
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288 </outputs>
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289
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290 <tests>
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291 <!-- Can also use assert_command to test command -->
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292 <!-- Testing GFF3 input -->
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293 <test>
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294 <param name="fasta_file" value="dbia3.fa"/>
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295 <repeat name="format">
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296 <conditional name="formatChoice">
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297 <param name="format_select" value="gff3"/>
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298 <param name="GFF3" value="augustusDbia3.gff3"/>
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299 </conditional>
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300 </repeat>
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301 <repeat name="format">
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302 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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303 <!-- TODO: Ask why the tests are not passing with this xml:
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304 Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history'
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305 <conditional name="formatChoice">
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306 <param name="format_select" value="bed"/>
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307 <conditional name="bedChoice">
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308 <param name="bed_select" value="bed_simple_repeats_option"/>
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309 <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/>
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310 </conditional>
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311 </conditional>
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312 -->
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313 </repeat>
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314
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315 <output name="output">
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316 <assert_contents>
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317 <has_text text="myHub"/>
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318 </assert_contents>
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319 <assert_contents>
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320 <has_text text="dbia3_trfBig.bb"/>
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321 </assert_contents>
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322 <assert_contents>
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323 <has_text text="SAODOAii qwwqod92921"/>
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324 </assert_contents>
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325 </output>
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326 </test>
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327 <test>
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328 <param name="fasta_file" value="dbia3.fa"/>
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329 <param name="GFF3" value="augustusDbia3.gff3"/>
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330 <output name="output" file="augustusOutput.html" lines_diff="2">
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331 <extra_files type="directory" value="myHub"/>
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332 <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/>
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333 </output>
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334 </test>
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335 <!-- Testing Generic BED input -->
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336 <!-- Testing Bed Simple repeat input -->
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337 </tests>
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338
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339 <help>
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340 This Galaxy tool permits to prepare your files to be ready for
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341 Assembly Hub visualization.
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342 </help>
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343 </tool>