Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 38:3a3591cf27f9 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 16:28:21 -0400
parents 046c5bfc0413
children 75edbc203532
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1 <tool id="jbrowse_hub" name="JBrowse Hub Creator" version="1.0">
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2 <description>
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3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
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4 </description>
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6 <requirements>
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7 <requirement type="package" version="1.2">samtools</requirement>
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8 <requirement type="package" version="1.9">numpy</requirement>
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9 <requirement type="package" version="1.68">biopython</requirement>
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10 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
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11 <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
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12 </requirements>
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14 <stdio>
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15 </stdio>
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17 <command detect_errors="exit_code"><![CDATA[
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18 python $__tool_directory__/jbrowse_hub.py
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19 --fasta '$reference'
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20 --genome_name '$genome_name'
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22 ## json metadata recording from Remi's hub-archive-creator.xml
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23 #import json
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24 #set global data_parameter_dict = {}
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25
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26 ## Function to retrieve the data of the inputs
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27 #def prepare_json($input_to_prepare, $extra_data_dict={})
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28 #set false_path = str($input_to_prepare)
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29 #set name = $input_to_prepare.name
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31 #set data_dict = {"name": $name}
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32 #silent data_dict.update($extra_data_dict)
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34 #silent $data_parameter_dict.update({$false_path: $data_dict})
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36 #end def
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39 #for $f in $format
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40 #set track_label = str($f.formatChoice.label)
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41 #set track_color = str($f.formatChoice.track_color)
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42 #set extra_data_dict = {"label" : $track_label,
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43 "track_color" : $track_color}
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44 #if $f.formatChoice.format_select == 'bed'
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45 #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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46 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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47 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
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48 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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49 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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50 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
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51 #end if
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52 #end if
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53 #if $f.formatChoice.format_select == 'bam'
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54 --bam $f.formatChoice.BAM
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55 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
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56 #end if
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57 #if $f.formatChoice.format_select == 'gff3'
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58 #set track_type = $f.formatChoice.track_type
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59 #silent extra_data_dict.update({"track_type" : $track_type})
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60 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
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61 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
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62 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
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63 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
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64 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
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65 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
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66 #end if
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67 #end if
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68 #if $f.formatChoice.format_select == 'blastxml'
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69 #set track_type = $f.formatChoice.track_type
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70 #silent extra_data_dict.update({"track_type" : $track_type})
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71 --blastxml $f.formatChoice.BlastXML
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72 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
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73 #end if
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74 #if $f.formatChoice.format_select == 'gtf'
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75 --gtf $f.formatChoice.GTF
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76 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
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77 #end if
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78 #if $f.formatChoice.format_select == 'bigwig'
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79 --bigwig $f.formatChoice.BIGWIG
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80 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
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81 #end if
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82 #end for
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84 #set all_data_json = json.dumps($data_parameter_dict)
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85 -j '$all_data_json'
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86 -e '$output.extra_files_path'
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87 -o '$output'
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88
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89 ]]></command>
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90
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91 <inputs>
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92 <param name="reference" type="data" format="fasta" label="Reference Genome" />
5
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93 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
0
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94 <repeat name="format" title="New track">
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95 <conditional name="formatChoice">
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96 <param name="format_select" type="select" label="Format">
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97 <option value="bam" selected="true">BAM</option>
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98 <option value="bed">BED</option>
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99 <option value="blastxml">BLASTXML</option>
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100 <option value="bigwig">BIGWIG</option>
12
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101 <option value="gff3_transcript">GFF3 (structure: gene->transcript->CDS)</option>
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102 <option value="gff3_mrna">GFF3 (structure: gene->mRNA->CDS)</option>
0
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103 <option value="gtf">GTF</option>
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104 </param>
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105
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106 <when value="bam">
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107 <param
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108 format="bam"
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109 name="BAM"
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110 type="data"
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111 label="BAM File"
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112 />
37
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113 <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" />
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114 <param name="track_color" type="color" label="Track color" value="#daa520">
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115 <sanitizer>
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116 <valid initial="string.letters,string.digits">
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117 <add value="#"/>
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118 </valid>
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119 </sanitizer>
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120 </param>
0
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121 </when>
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122 <when value="bed">
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123 <conditional name="bedChoice">
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124 <param name="bed_select" type="select" label="Bed Choice">
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125 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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126 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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127 </param>
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128 <when value="bed_simple_repeats_option">
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129 <param
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130 format="bed"
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131 name="BED_simple_repeats"
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132 type="data"
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133 label="Bed Simple Repeats (Bed4+12) File"
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134 />
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135 </when>
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136 <when value="bed_splice_junctions_option">
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137 <param
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138 format="bed"
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139 name="BED_splice_junctions"
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140 type="data"
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141 label="Bed Splice Junctions (Bed12+1) File"
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142 />
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143 </when>
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144 </conditional>
37
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145 <param name="label" type="text" size="30" value="BED file" label="Track name" />
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146 <param name="track_color" type="color" label="Track color" value="#daa520">
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147 <sanitizer>
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148 <valid initial="string.letters,string.digits">
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149 <add value="#"/>
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150 </valid>
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151 </sanitizer>
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152 </param>
0
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153 </when>
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154 <when value="blastxml">
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155 <param
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156 format="blastxml"
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157 name="BlastXML"
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158 type="data"
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159 label="Blast Alignments File"
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160 />
37
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161 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
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162 <param name="track_type" type="select" label="Set trackType">
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163 <option value="CanvasFeatures">CanvasFeatures (Default)</option>
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164 <option value="G-OnRamp_plugin/BlastAlignment">BlastAlignment (contain advanced features, need install G_OnRamp_plugin</option>
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165 </param>
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166 <param name="track_color" type="color" label="Track color" value="#daa520">
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167 <sanitizer>
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168 <valid initial="string.letters,string.digits">
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169 <add value="#"/>
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170 </valid>
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171 </sanitizer>
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172 </param>
0
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173 </when>
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174 <when value="bigwig">
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175 <param
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176 format="bigwig"
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177 name="BIGWIG"
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178 type="data"
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179 label="BIGWIG File"
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180 />
37
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181 <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" />
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182 <param name="track_color" type="color" label="Track color" value="#daa520">
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183 <sanitizer>
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184 <valid initial="string.letters,string.digits">
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185 <add value="#"/>
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186 </valid>
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187 </sanitizer>
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188 </param>
0
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189 </when>
31
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190 <when value="gff3">
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191 <conditional name="gff3Choice">
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192 <param name="gff3_select" type="select" label="gff3 type">
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193 <option value="gff3_transcript">GFF3 format, structure: gene->transcription->CDS</option>
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194 <option value="gff3_mrna">GFF3 format, structure: gene->mRNA->CDS</option>
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195 </param>
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196 <when value="gff3_transcript">
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197 <param
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198 format="gff3"
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199 name="GFF3_transcript"
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200 type="data"
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201 label="GFF3 File"
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202 />
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203 </when>
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204 <when value="gff3_mrna">
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205 <param
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206 format="gff3"
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207 name="GFF3_mrna"
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208 type="data"
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209 label="GFF3 File"
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210 />
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211 </when>
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212 </conditional>
37
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213 <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" />
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214 <param name="track_type" type="select" label="Set trackType">
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215 <option value="CanvasFeatures">CanvasFeatures (Default)</option>
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216 <option value="G-OnRamp_plugin/GenePred">GenePred (contain advanced features, need install G_OnRamp_plugin</option>
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217 </param>
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218 <param name="track_color" type="color" label="Track color" value="#daa520">
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219 <sanitizer>
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220 <valid initial="string.letters,string.digits">
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221 <add value="#"/>
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222 </valid>
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223 </sanitizer>
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224 </param>
0
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225 </when>
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226 <when value="gtf">
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227 <param
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228 format="gtf"
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229 name="GTF"
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230 type="data"
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231 label="GTF File"
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232 />
37
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233 <param name="label" type="text" size="30" value="Assembled Transcripts" label="Track name" />
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234 <param name="track_color" type="color" label="Track color" value="#daa520">
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235 <sanitizer>
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236 <valid initial="string.letters,string.digits">
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237 <add value="#"/>
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238 </valid>
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239 </sanitizer>
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240 </param>
0
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241 </when>
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242 </conditional>
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243 </repeat>
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244 </inputs>
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245
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246 <outputs>
5
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247 <data format="html" name="output" label="${tool.name}" />
0
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248 </outputs>
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249 <tests>
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250 <test>
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251 <param name="reference" value="dbia3/raw/dbia3.fa" />
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252 <param name="output" value="hubtest" />
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253 <repeat name="format">
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254 <conditional name="formatChoice">
15
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255 <param name="format_select" value="gff3_transcript"/>
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256 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
0
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257 </conditional>
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258 </repeat>
5
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259 <output name="output" file="hubtest" >
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260 </output>
0
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261 </test>
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262 </tests>
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263 <help>
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264 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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265 JBrowse visualization.
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266 </help>
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267 <citations>
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268 </citations>
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269 </tool>