Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 47:b7bf45272ab7 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 73ede51a133dc8914812195a1b4cd512bfb8f23d-dirty
author yating-l
date Wed, 22 Mar 2017 15:20:56 -0400
parents b32f9f4793f8
children 6803152ea92a
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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 '$genome_name'
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22 ## json metadata recording from Remi's hub-archive-creator.xml
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23 #import json
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24 #set global data_parameter_dict = {}
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26 ## Function to retrieve the data of the inputs
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27 #def prepare_json($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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37
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38 #for $g in $group
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39 #for $f in $g.format
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40 #set track_label = str($f.formatChoice.label)
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41 #set group_name = str($g.group_name)
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42 #set extra_data_dict = {"label" : $track_label, "category" : $group_name}
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43 #if $f.formatChoice.format_select == 'bed'
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44 #set track_color = str($f.formatChoice.track_color)
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45 #silent extra_data_dict.update({"color" : $track_color})
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46 #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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47 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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48 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
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49 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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50 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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51 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
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52 #end if
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53 #end if
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54 #if $f.formatChoice.format_select == 'bam'
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55 --bam $f.formatChoice.BAM
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56 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
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57 #end if
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58 #if $f.formatChoice.format_select == 'gff3'
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59 #set track_color = str($f.formatChoice.track_color)
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60 #silent extra_data_dict.update({"color" : $track_color})
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61 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
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62 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
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63 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
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64 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
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65 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
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66 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
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67 #end if
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68 #end if
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69 #if $f.formatChoice.format_select == 'blastxml'
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70 --blastxml $f.formatChoice.BlastXML
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71 #set track_color = str($f.formatChoice.track_color)
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72 #silent extra_data_dict.update({"color" : $track_color})
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73 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
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74 #end if
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75 #if $f.formatChoice.format_select == 'gtf'
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76 --gtf $f.formatChoice.GTF
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77 #set track_color = str($f.formatChoice.track_color)
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78 #silent extra_data_dict.update({"color" : $track_color})
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79 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
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80 #end if
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81 #if $f.formatChoice.format_select == 'bigwig'
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82 --bigwig $f.formatChoice.BIGWIG
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83 #set pos_color = str($f.formatChoice.pos_color)
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84 #set neg_color = str($f.formatChoice.neg_color)
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85 #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
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86 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
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87 #end if
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88 #end for
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89 #end for
31
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90
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91 #set all_data_json = json.dumps($data_parameter_dict)
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92 -j '$all_data_json'
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93 -e '$output.extra_files_path'
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94 -o '$output'
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95
0
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96 ]]></command>
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97
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98 <inputs>
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99 <param name="reference" type="data" format="fasta" label="Reference Genome" />
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100 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
42
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101 <repeat name="group" title="New group">
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102 <param type="text" name="group_name" label="Group name" value="Default group"/>
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103 <repeat name="format" title="New track">
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104 <conditional name="formatChoice">
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105 <param name="format_select" type="select" label="Format">
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106 <option value="bam" selected="true">BAM</option>
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107 <option value="bed">BED</option>
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108 <option value="blastxml">BLASTXML</option>
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109 <option value="bigwig">BIGWIG</option>
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110 <option value="gff3">GFF3</option>
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111 <option value="gtf">GTF</option>
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112 </param>
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113
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114 <when value="bam">
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115 <param
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116 format="bam"
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117 name="BAM"
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118 type="data"
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119 label="BAM File"
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120 />
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121 <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" />
0
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122 </when>
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123 <when value="bed">
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124 <conditional name="bedChoice">
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125 <param name="bed_select" type="select" label="Bed Choice">
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126 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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127 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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128 </param>
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129 <when value="bed_simple_repeats_option">
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130 <param
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131 format="bed"
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132 name="BED_simple_repeats"
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133 type="data"
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134 label="Bed Simple Repeats (Bed4+12) File"
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135 />
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136 </when>
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137 <when value="bed_splice_junctions_option">
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138 <param
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139 format="bed"
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140 name="BED_splice_junctions"
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141 type="data"
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142 label="Bed Splice Junctions (Bed12+1) File"
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143 />
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144 </when>
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145 </conditional>
37
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146 <param name="label" type="text" size="30" value="BED file" label="Track name" />
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147 <param name="track_color" type="color" label="Track color" value="#daa520">
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148 <sanitizer>
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149 <valid initial="string.letters,string.digits">
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150 <add value="#"/>
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151 </valid>
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152 </sanitizer>
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153 </param>
0
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154 </when>
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155 <when value="blastxml">
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156 <param
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157 format="blastxml"
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158 name="BlastXML"
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159 type="data"
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160 label="Blast Alignments File"
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161 />
37
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162 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
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163 <param name="track_color" type="color" label="Track color" value="#daa520">
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164 <sanitizer>
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165 <valid initial="string.letters,string.digits">
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166 <add value="#"/>
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167 </valid>
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168 </sanitizer>
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169 </param>
0
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170 </when>
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171 <when value="bigwig">
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172 <param
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173 format="bigwig"
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174 name="BIGWIG"
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175 type="data"
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176 label="BIGWIG File"
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177 />
37
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178 <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" />
39
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179 <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600">
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180 <sanitizer>
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181 <valid initial="string.letters,string.digits">
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182 <add value="#"/>
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183 </valid>
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184 </sanitizer>
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185 </param>
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186 <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF">
37
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187 <sanitizer>
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188 <valid initial="string.letters,string.digits">
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189 <add value="#"/>
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190 </valid>
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191 </sanitizer>
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192 </param>
0
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193 </when>
31
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194 <when value="gff3">
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195 <conditional name="gff3Choice">
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196 <param name="gff3_select" type="select" label="gff3 type">
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197 <option value="gff3_transcript">GFF3 format, structure: gene->transcription->CDS</option>
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198 <option value="gff3_mrna">GFF3 format, structure: gene->mRNA->CDS</option>
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199 </param>
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200 <when value="gff3_transcript">
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201 <param
41
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202 format="gff3"
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203 name="GFF3_transcript"
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204 type="data"
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205 label="GFF3 File"
31
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206 />
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207 </when>
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208 <when value="gff3_mrna">
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209 <param
41
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210 format="gff3"
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211 name="GFF3_mrna"
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212 type="data"
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213 label="GFF3 File"
31
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214 />
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215 </when>
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216 </conditional>
37
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217 <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" />
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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>
42
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242 </conditional>
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243 </repeat>
0
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244 </repeat>
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245 </inputs>
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246
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247 <outputs>
5
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248 <data format="html" name="output" label="${tool.name}" />
0
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249 </outputs>
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250 <tests>
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251 <test>
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252 <param name="reference" value="dbia3/raw/dbia3.fa" />
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253 <param name="output" value="hubtest" />
43
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254 <repeat name="group">
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255 <param name="group_name" value="Default group"/>
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256 <repeat name="format">
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257 <conditional name="formatChoice">
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258 <param name="format_select" value="gff3_transcript"/>
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259 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
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260 </conditional>
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261 </repeat>
0
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262 </repeat>
5
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263 <output name="output" file="hubtest" >
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264 </output>
0
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265 </test>
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266 </tests>
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267 <help>
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268 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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269 JBrowse visualization.
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270 </help>
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271 <citations>
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272 </citations>
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273 </tool>