Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 2:d048f9f9f9df draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Fri, 10 Mar 2017 14:27:54 -0500
parents 472f074fbf1f
children e7c80e9b70ae
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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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5
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6 <requirements>
2
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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 </requirements>
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10
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11 <stdio>
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12 </stdio>
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13
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14 <command detect_errors="exit_code"><![CDATA[
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15 python $__tool_directory__/jbrowse_hub.py
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16 --fasta '$reference'
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17 #for $f in $format
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18 #if $f.formatChoice.format_select == 'bed'
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19 #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
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20 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
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21 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
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22 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
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23 #end if
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24 #end if
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25 #if $f.formatChoice.format_select == 'bam'
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26 --bam $f.formatChoice.BAM
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27 #end if
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28 #if $f.formatChoice.format_select == 'gff3'
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29 --gff3 $f.formatChoice.GFF3
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30 #end if
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31 #if $f.formatChoice.format_select == 'blastxml'
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32 --blastxml $f.formatChoice.BlastXML
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33 #end if
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34 #if $f.formatChoice.format_select == 'gtf'
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35 --gtf $f.formatChoice.GTF
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36 #end if
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37 #if $f.formatChoice.format_select == 'bigwig'
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38 --bigwig $f.formatChoice.BIGWIG
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39 #end if
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40 #end for
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41 --out $output
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42 ]]></command>
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43
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44 <inputs>
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45 <param name="reference" type="data" format="fasta" label="Reference Genome" />
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46 <param name="output" type="text" size="30" value="unknown" label="Output folder" />
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47 <repeat name="format" title="New track">
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48 <conditional name="formatChoice">
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49 <param name="format_select" type="select" label="Format">
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50 <option value="bam" selected="true">BAM</option>
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51 <option value="bed">BED</option>
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52 <option value="blastxml">BLASTXML</option>
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53 <option value="bigwig">BIGWIG</option>
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54 <option value="gff3">GFF3</option>
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55 <option value="gtf">GTF</option>
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56 </param>
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57
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58 <when value="bam">
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59 <param
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60 format="bam"
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61 name="BAM"
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62 type="data"
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63 label="BAM File"
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64 />
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65 </when>
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66 <when value="bed">
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67 <conditional name="bedChoice">
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68 <param name="bed_select" type="select" label="Bed Choice">
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69 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
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70 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
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71 </param>
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72 <when value="bed_simple_repeats_option">
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73 <param
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74 format="bed"
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75 name="BED_simple_repeats"
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76 type="data"
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77 label="Bed Simple Repeats (Bed4+12) File"
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78 />
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79 </when>
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80 <when value="bed_splice_junctions_option">
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81 <param
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82 format="bed"
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83 name="BED_splice_junctions"
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84 type="data"
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85 label="Bed Splice Junctions (Bed12+1) File"
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86 />
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87 </when>
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88 </conditional>
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89 </when>
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90 <when value="blastxml">
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91 <param
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92 format="blastxml"
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93 name="BlastXML"
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94 type="data"
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95 label="Blast Alignments File"
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96 />
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97 </when>
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98 <when value="bigwig">
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99 <param
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100 format="bigwig"
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101 name="BIGWIG"
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102 type="data"
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103 label="BIGWIG File"
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104 />
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105 </when>
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106 <when value="gff3">
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107 <param
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108 format="gff3"
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109 name="GFF3"
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110 type="data"
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111 label="GFF3 File"
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112 />
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113 </when>
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114 <when value="gtf">
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115 <param
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116 format="gtf"
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117 name="GTF"
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118 type="data"
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119 label="GTF File"
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120 />
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121 </when>
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122 </conditional>
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123 </repeat>
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124 </inputs>
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125
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126 <outputs>
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127 <data format="tar" name="JBrowseHub" label="${tool.name} on ${output}" />
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128 </outputs>
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129 <tests>
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130 <test>
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131 <param name="reference" value="dbia3/raw/dbia3.fa" />
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132 <param name="output" value="hubtest" />
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133 <repeat name="format">
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134 <conditional name="formatChoice">
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135 <param name="format_select" value="gff3"/>
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136 <param name="GFF3" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
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137 </conditional>
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138 </repeat>
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139 <output name="JBrowseHub" file="hubtest.tar" />
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140 </test>
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141 </tests>
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142 <help>
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143 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
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144 JBrowse visualization.
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145 </help>
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146 <citations>
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147 </citations>
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148 </tool>