Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 62:86d6f50870dd draft default tip

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 79699b5964c673b7eb815b4d669ab7f07ea2068a-dirty
author yating-l
date Tue, 11 Apr 2017 16:08:57 -0400
parents ea301a2d2229
children
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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 '$genome_name'
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22 #set galaxy_url = str($GALAXY_URL)
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23 #set $jbrowse_url = galaxy_url.replace("8080", "80")
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24 --jbrowse_host '$jbrowse_url'
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26 ## json metadata recording from Remi's hub-archive-creator.xml
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27 #import json
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28 #set global data_parameter_dict = {}
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30 ## Function to retrieve the data of the inputs
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31 #def prepare_json($input_to_prepare, $extra_data_dict={})
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32 #set false_path = str($input_to_prepare)
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33 #set name = $input_to_prepare.name
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35 #set data_dict = {"name": $name}
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36 #silent data_dict.update($extra_data_dict)
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38 #silent $data_parameter_dict.update({$false_path: $data_dict})
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40 #end def
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42 #for $g in $group
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43 #for $f in $g.format
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44 #set track_label = str($f.formatChoice.label)
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45 #set group_name = str($g.group_name)
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46 #set extra_data_dict = {"label" : $track_label, "category" : $group_name}
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47 #if $f.formatChoice.format_select == 'bed'
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48 #set track_color = str($f.formatChoice.track_color)
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49 #silent extra_data_dict.update({"color" : $track_color})
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50 #if $f.formatChoice.bedChoice.bed_select == 'bed_generic_option'
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51 --bed $f.formatChoice.bedChoice.BED_generic
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52 #silent $prepare_json($f.formatChoice.bedChoice.BED_generic, extra_data_dict)
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53 #elif $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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54 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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55 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
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56 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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57 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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58 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
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59 #end if
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60 #end if
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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 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
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64 #end if
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65 #if $f.formatChoice.format_select == 'gff3'
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66 #set track_color = str($f.formatChoice.track_color)
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67 #silent extra_data_dict.update({"color" : $track_color})
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68 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic'
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69 --gff3 $f.formatChoice.gff3Choice.GFF3_generic
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70 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_generic, extra_data_dict)
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71 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
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72 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
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73 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
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74 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
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75 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
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76 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
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77 #end if
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78 #end if
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79 #if $f.formatChoice.format_select == 'blastxml'
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80 --blastxml $f.formatChoice.BlastXML
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81 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
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82 #end if
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83 #if $f.formatChoice.format_select == 'gtf'
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84 --gtf $f.formatChoice.GTF
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85 #set track_color = str($f.formatChoice.track_color)
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86 #silent extra_data_dict.update({"color" : $track_color})
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87 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
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88 #end if
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89 #if $f.formatChoice.format_select == 'bigwig'
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90 --bigwig $f.formatChoice.BIGWIG
39
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91 #set pos_color = str($f.formatChoice.pos_color)
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92 #set neg_color = str($f.formatChoice.neg_color)
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93 #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
31
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94 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
0
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95 #end if
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96 #end for
42
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97 #end for
31
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98
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99 #set all_data_json = json.dumps($data_parameter_dict)
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100 -j '$all_data_json'
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101 -e '$output.extra_files_path'
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102 -o '$output'
31
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103
0
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104 ]]></command>
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105
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106 <inputs>
60
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107 <param name="GALAXY_URL" type="baseurl" value="" />
0
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108 <param name="reference" type="data" format="fasta" label="Reference Genome" />
5
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109 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
42
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110 <repeat name="group" title="New group">
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111 <param type="text" name="group_name" label="Group name" value="Default group"/>
0
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112 <repeat name="format" title="New track">
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113 <conditional name="formatChoice">
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114 <param name="format_select" type="select" label="Format">
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115 <option value="bam" selected="true">BAM</option>
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116 <option value="bed">BED</option>
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117 <option value="blastxml">BLASTXML</option>
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118 <option value="bigwig">BIGWIG</option>
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119 <option value="gff3">GFF3</option>
0
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120 <option value="gtf">GTF</option>
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121 </param>
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122
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123 <when value="bam">
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124 <param
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125 format="bam"
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126 name="BAM"
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127 type="data"
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128 label="BAM File"
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129 />
37
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130 <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" />
0
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131 </when>
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132 <when value="bed">
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133 <conditional name="bedChoice">
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134 <param name="bed_select" type="select" label="Bed Choice">
50
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135 <option value="bed_generic_option">BED format</option>
0
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136 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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137 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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138 </param>
50
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139 <when value="bed_generic_option">
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140 <param
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141 format="bed"
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142 name="BED_generic"
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143 type="data"
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144 label="Bed File"
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145 />
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146 </when>
0
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147 <when value="bed_simple_repeats_option">
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148 <param
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149 format="bed"
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150 name="BED_simple_repeats"
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151 type="data"
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152 label="Bed Simple Repeats (Bed4+12) File"
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153 />
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154 </when>
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155 <when value="bed_splice_junctions_option">
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156 <param
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157 format="bed"
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158 name="BED_splice_junctions"
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159 type="data"
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160 label="Bed Splice Junctions (Bed12+1) File"
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161 />
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162 </when>
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163 </conditional>
37
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164 <param name="label" type="text" size="30" value="BED file" label="Track name" />
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165 <param name="track_color" type="color" label="Track color" value="#daa520">
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166 <sanitizer>
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167 <valid initial="string.letters,string.digits">
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168 <add value="#"/>
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169 </valid>
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170 </sanitizer>
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171 </param>
0
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172 </when>
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173 <when value="blastxml">
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174 <param
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175 format="blastxml"
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176 name="BlastXML"
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177 type="data"
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178 label="Blast Alignments File"
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179 />
37
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180 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
0
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181 </when>
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182 <when value="bigwig">
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183 <param
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184 format="bigwig"
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185 name="BIGWIG"
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186 type="data"
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187 label="BIGWIG File"
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188 />
37
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189 <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" />
39
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190 <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600">
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191 <sanitizer>
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192 <valid initial="string.letters,string.digits">
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193 <add value="#"/>
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194 </valid>
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195 </sanitizer>
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196 </param>
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197 <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF">
37
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198 <sanitizer>
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199 <valid initial="string.letters,string.digits">
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200 <add value="#"/>
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201 </valid>
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202 </sanitizer>
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203 </param>
0
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204 </when>
31
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205 <when value="gff3">
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206 <conditional name="gff3Choice">
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207 <param name="gff3_select" type="select" label="gff3 type">
50
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208 <option value="gff3_generic">GFF3 format</option>
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209 <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option>
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210 <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option>
31
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211 </param>
50
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212 <when value="gff3_generic">
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213 <param
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214 format="gff3"
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215 name="GFF3_generic"
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216 type="data"
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217 label="GFF3 File"
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218 />
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219 </when>
31
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220 <when value="gff3_transcript">
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221 <param
41
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222 format="gff3"
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223 name="GFF3_transcript"
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224 type="data"
50
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225 label="GFF3 File from gene prediction"
31
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226 />
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227 </when>
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228 <when value="gff3_mrna">
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229 <param
41
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230 format="gff3"
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231 name="GFF3_mrna"
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232 type="data"
50
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233 label="GFF3 File from gene prediction"
31
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234 />
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235 </when>
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236 </conditional>
37
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237 <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" />
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238 <param name="track_color" type="color" label="Track color" value="#daa520">
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239 <sanitizer>
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240 <valid initial="string.letters,string.digits">
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241 <add value="#"/>
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242 </valid>
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243 </sanitizer>
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244 </param>
0
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245 </when>
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246 <when value="gtf">
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247 <param
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248 format="gtf"
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249 name="GTF"
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250 type="data"
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251 label="GTF File"
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252 />
37
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253 <param name="label" type="text" size="30" value="Assembled Transcripts" label="Track name" />
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254 <param name="track_color" type="color" label="Track color" value="#daa520">
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255 <sanitizer>
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256 <valid initial="string.letters,string.digits">
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257 <add value="#"/>
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258 </valid>
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259 </sanitizer>
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260 </param>
0
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261 </when>
42
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262 </conditional>
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263 </repeat>
0
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264 </repeat>
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265 </inputs>
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266
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267 <outputs>
5
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268 <data format="html" name="output" label="${tool.name}" />
0
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269 </outputs>
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270 <tests>
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271 <test>
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272 <param name="reference" value="dbia3/raw/dbia3.fa" />
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273 <param name="output" value="hubtest" />
43
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274 <repeat name="group">
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275 <param name="group_name" value="Default group"/>
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276 <repeat name="format">
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277 <conditional name="formatChoice">
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278 <param name="format_select" value="gff3_transcript"/>
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279 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
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280 </conditional>
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281 </repeat>
0
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282 </repeat>
5
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283 <output name="output" file="hubtest" >
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284 </output>
0
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285 </test>
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286 </tests>
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287 <help>
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288 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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289 JBrowse visualization.
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290 </help>
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291 <citations>
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292 </citations>
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293 </tool>