Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 18:7a775b231676 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 15:24:13 -0400
parents 99d66676570b
children 2edc47a6d575
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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="1.9">numpy</requirement>
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8 <requirement type="package" version="1.68">biopython</requirement>
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9 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
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10 <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
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11 </requirements>
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12
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13 <stdio>
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14 </stdio>
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16 <command detect_errors="exit_code"><![CDATA[
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17 python $__tool_directory__/jbrowse_hub.py
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18 --fasta '$reference'
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19 #for $f in $format
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20 #if $f.formatChoice.format_select == 'bed'
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21 #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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22 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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23 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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24 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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25 #end if
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26 #end if
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27 #if $f.formatChoice.format_select == 'bam'
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28 --bam $f.formatChoice.BAM
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29 #end if
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30 #if $f.formatChoice.format_select == 'bai'
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31 --bai $f.formatChoice.BAI
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32 #end if
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33 #if $f.formatChoice.format_select == 'gff3_transcript'
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34 --gff3_transcript $f.formatChoice.GFF3_transcript
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35 #end if
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36 #if $f.formatChoice.format_select == 'gff3_mrna'
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37 --gff3_mrna $f.formatChoice.GFF3_mrna
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38 #end if
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39 #if $f.formatChoice.format_select == 'blastxml'
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40 --blastxml $f.formatChoice.BlastXML
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41 #end if
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42 #if $f.formatChoice.format_select == 'gtf'
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43 --gtf $f.formatChoice.GTF
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44 #end if
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45 #if $f.formatChoice.format_select == 'bigwig'
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46 --bigwig $f.formatChoice.BIGWIG
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47 #end if
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48 #end for
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49 --genome_name '$genome_name'
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50 -e '$output.extra_files_path'
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51 -o '$output'
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52 ]]></command>
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53
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54 <inputs>
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55 <param name="reference" type="data" format="fasta" label="Reference Genome" />
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56 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
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57 <repeat name="format" title="New track">
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58 <conditional name="formatChoice">
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59 <param name="format_select" type="select" label="Format">
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60 <option value="bam" selected="true">BAM</option>
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61 <option value="bai" selected="true">BAI (BAM index)</option>
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62 <option value="bed">BED</option>
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63 <option value="blastxml">BLASTXML</option>
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64 <option value="bigwig">BIGWIG</option>
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65 <option value="gff3_transcript">GFF3 (structure: gene->transcript->CDS)</option>
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66 <option value="gff3_mrna">GFF3 (structure: gene->mRNA->CDS)</option>
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67 <option value="gtf">GTF</option>
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68 </param>
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69
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70 <when value="bam">
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71 <param
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72 format="bam"
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73 name="BAM"
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74 type="data"
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75 label="BAM File"
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76 />
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77 </when>
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78 <when value="bai">
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79 <param
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80 format="bai"
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81 name="BAI"
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82 type="data"
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83 label="BAI File"
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84 />
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85 </when>
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86 <when value="bed">
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87 <conditional name="bedChoice">
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88 <param name="bed_select" type="select" label="Bed Choice">
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89 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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90 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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91 </param>
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92 <when value="bed_simple_repeats_option">
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93 <param
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94 format="bed"
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95 name="BED_simple_repeats"
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96 type="data"
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97 label="Bed Simple Repeats (Bed4+12) File"
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98 />
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99 </when>
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100 <when value="bed_splice_junctions_option">
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101 <param
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102 format="bed"
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103 name="BED_splice_junctions"
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104 type="data"
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105 label="Bed Splice Junctions (Bed12+1) File"
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106 />
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107 </when>
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108 </conditional>
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109 </when>
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110 <when value="blastxml">
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111 <param
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112 format="blastxml"
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113 name="BlastXML"
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114 type="data"
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115 label="Blast Alignments File"
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116 />
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117 </when>
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118 <when value="bigwig">
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119 <param
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120 format="bigwig"
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121 name="BIGWIG"
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122 type="data"
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123 label="BIGWIG File"
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124 />
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125 </when>
12
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126 <when value="gff3_transcript">
0
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127 <param
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128 format="gff3"
15
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129 name="GFF3_transcript"
12
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130 type="data"
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131 label="GFF3 File"
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132 />
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133 </when>
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134 <when value="gff3_mrna">
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135 <param
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136 format="gff3"
15
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137 name="GFF3_mrna"
0
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138 type="data"
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139 label="GFF3 File"
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140 />
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141 </when>
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142 <when value="gtf">
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143 <param
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144 format="gtf"
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145 name="GTF"
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146 type="data"
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147 label="GTF File"
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148 />
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149 </when>
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150 </conditional>
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151 </repeat>
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152 </inputs>
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153
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154 <outputs>
5
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155 <data format="html" name="output" label="${tool.name}" />
0
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156 </outputs>
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157 <tests>
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158 <test>
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159 <param name="reference" value="dbia3/raw/dbia3.fa" />
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160 <param name="output" value="hubtest" />
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161 <repeat name="format">
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162 <conditional name="formatChoice">
15
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163 <param name="format_select" value="gff3_transcript"/>
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164 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
0
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165 </conditional>
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166 </repeat>
5
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167 <output name="output" file="hubtest" >
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168 </output>
0
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169 </test>
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170 </tests>
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171 <help>
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172 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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173 JBrowse visualization.
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174 </help>
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175 <citations>
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176 </citations>
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177 </tool>